SNP Links for Gene (Select 79652) - SNP

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Select item 14915193561.

rs1491519356 has merged into rs4017983 [Homo sapiens]

Variant type:: DELINS
Alleles:: CACA>-,CA,CACACA,CACACACA,CACACATTCACATGCATGCACACACACACA,CACACGCACACACACACA [Show Flanks]
Chromosome:: 16:1528440 (GRCh38)
16:1578441 (GRCh37)
Canonical SPDI:: NC_000016.10:1528433:CACACACACA:CACACA,NC_000016.10:1528433:CACACACACA:CACACACA,NC_000016.10:1528433:CACACACACA:CACACACACACA,NC_000016.10:1528433:CACACACACA:CACACACACACACA,NC_000016.10:1528433:CACACACACA:CACACACACACATTCACATGCATGCACACACACACA,NC_000016.10:1528433:CACACACACA:CACACACACACGCACACACACACA
Gene:: IFT140 (Varview), TMEM204 (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,genic_downstream_transcript_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: CACACACA=0./0 (ALFA)
CA=0.34068/340 (GoNL)
CA=0.36242/216 (NorthernSweden)
-=0.41891/6994 (TOMMO)
-=0.44888/2248 (1000Genomes)
HGVS:: NC_000016.10:g.1528434CA[3], NC_000016.10:g.1528434CA[4], NC_000016.10:g.1528434CA[6], NC_000016.10:g.1528434CA[7], NC_000016.10:g.1528434_1528443CA[6]TTCACATGCATGCACACACACACA[1], NC_000016.10:g.1528434_1528443CA[5]CGCACACACACACA[1], NC_000016.9:g.1578435CA[3], NC_000016.9:g.1578435CA[4], NC_000016.9:g.1578435CA[6], NC_000016.9:g.1578435CA[7], NC_000016.9:g.1578435_1578444CA[6]TTCACATGCATGCACACACACACA[1], NC_000016.9:g.1578435_1578444CA[5]CGCACACACACACA[1], NG_032783.1:g.88666TG[3], NG_032783.1:g.88666TG[4], NG_032783.1:g.88666TG[6], NG_032783.1:g.88666TG[7], NG_032783.1:g.88666_88675TG[6]CATG[2]TGAATGTGTGTGTGTG[1], NG_032783.1:g.88666_88675TG[6]CGTGTGTGTGTG[1]

Select item 14912192322.

rs1491219232 has merged into rs1043234759 [Homo sapiens]

Variant type:: DELINS
Alleles:: ACACACAC>-,ACAC,ACACAC,ACACACACAC,ACACACACACAC [Show Flanks]
Chromosome:: 16:1528363 (GRCh38)
16:1578364 (GRCh37)
Canonical SPDI:: NC_000016.10:1528361:CACACACAC:C,NC_000016.10:1528361:CACACACAC:CACAC,NC_000016.10:1528361:CACACACAC:CACACAC,NC_000016.10:1528361:CACACACAC:CACACACACAC,NC_000016.10:1528361:CACACACAC:CACACACACACAC
Gene:: IFT140 (Varview), TMEM204 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant,intron_variant,genic_downstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: CACAC=0./0 (ALFA)
CA=0.00014/2 (TOMMO)
HGVS:: NC_000016.10:g.1528363_1528370del, NC_000016.10:g.1528363AC[2], NC_000016.10:g.1528363AC[3], NC_000016.10:g.1528363AC[5], NC_000016.10:g.1528363AC[6], NC_000016.9:g.1578364_1578371del, NC_000016.9:g.1578364AC[2], NC_000016.9:g.1578364AC[3], NC_000016.9:g.1578364AC[5], NC_000016.9:g.1578364AC[6], NG_032783.1:g.88740_88747del, NG_032783.1:g.88740TG[2], NG_032783.1:g.88740TG[3], NG_032783.1:g.88740TG[5], NG_032783.1:g.88740TG[6]

Select item 14909553313.

rs1490955331 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 16:1526863 (GRCh38)
16:1576864 (GRCh37)
Canonical SPDI:: NC_000016.10:1526862:C:T
Gene:: IFT140 (Varview), TMEM204 (Varview)
Functional Consequence:: 2KB_upstream_variant,genic_downstream_transcript_variant,intron_variant,upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000011/3 (TOPMED)
HGVS:: NC_000016.10:g.1526863C>T, NC_000016.9:g.1576864C>T, NG_032783.1:g.90246G>A

Select item 14908447144.

rs1490844714 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 16:1538042 (GRCh38)
16:1588043 (GRCh37)
Canonical SPDI:: NC_000016.10:1538041:C:T
Gene:: IFT140 (Varview), TMEM204 (Varview)
Functional Consequence:: 3_prime_UTR_variant,genic_downstream_transcript_variant,intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000004/1 (TOPMED)
HGVS:: NC_000016.10:g.1538042C>T, NC_000016.9:g.1588043C>T, NG_032783.1:g.79067G>A, XM_011522772.4:c.*2684G>A, XM_011522772.1:c.*2684G>A, XM_047434976.1:c.*2684G>A, XM_047434972.1:c.*1623G>A

Select item 14904898885.

rs1490489888 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 16:1544143 (GRCh38)
16:1594144 (GRCh37)
Canonical SPDI:: NC_000016.10:1544142:G:A
Gene:: IFT140 (Varview), TMEM204 (Varview)
Functional Consequence:: genic_downstream_transcript_variant,intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000007/1 (GnomAD)
A=0.000011/3 (TOPMED)
HGVS:: NC_000016.10:g.1544143G>A, NC_000016.9:g.1594144G>A, NG_032783.1:g.72966C>T

Select item 14903805606.

rs1490380560 [Homo sapiens]

Variant type:: SNV
Alleles:: G>C [Show Flanks]
Chromosome:: 16:1531432 (GRCh38)
16:1581433 (GRCh37)
Canonical SPDI:: NC_000016.10:1531431:G:C
Gene:: IFT140 (Varview), TMEM204 (Varview)
Functional Consequence:: 5_prime_UTR_variant,genic_downstream_transcript_variant,intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000019/5 (TOPMED)
C=0.000021/3 (GnomAD)
G=0.5/1 (SGDP_PRJ)
HGVS:: NC_000016.10:g.1531432G>C, NC_000016.9:g.1581433G>C, NG_032783.1:g.85677C>G, XM_006720992.4:c.-2492C>G

Select item 14902323677.

rs1490232367 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A [Show Flanks]
Chromosome:: 16:1532552 (GRCh38)
16:1582553 (GRCh37)
Canonical SPDI:: NC_000016.10:1532551:C:A
Gene:: IFT140 (Varview), TMEM204 (Varview)
Functional Consequence:: upstream_transcript_variant,genic_downstream_transcript_variant,intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000004/1 (TOPMED)
HGVS:: NC_000016.10:g.1532552C>A, NC_000016.9:g.1582553C>A, NG_032783.1:g.84557G>T

Select item 14902162098.

rs1490216209 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 16:1531786 (GRCh38)
16:1581787 (GRCh37)
Canonical SPDI:: NC_000016.10:1531785:T:C
Gene:: IFT140 (Varview), TMEM204 (Varview)
Functional Consequence:: intron_variant,genic_upstream_transcript_variant,upstream_transcript_variant,genic_downstream_transcript_variant,5_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000007/1 (GnomAD)
C=0.000015/4 (TOPMED)
HGVS:: NC_000016.10:g.1531786T>C, NC_000016.9:g.1581787T>C, NG_032783.1:g.85323A>G, XM_006720992.4:c.-2846A>G

Select item 14901278619.

rs1490127861 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 16:1528575 (GRCh38)
16:1578576 (GRCh37)
Canonical SPDI:: NC_000016.10:1528574:A:G
Gene:: IFT140 (Varview), TMEM204 (Varview)
Functional Consequence:: 2KB_upstream_variant,genic_downstream_transcript_variant,intron_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.00003/8 (TOPMED)
G=0.000036/5 (GnomAD)
HGVS:: NC_000016.10:g.1528575A>G, NC_000016.9:g.1578576A>G, NG_032783.1:g.88534T>C

Select item 149012292410.

rs1490122924 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 16:1530255 (GRCh38)
16:1580256 (GRCh37)
Canonical SPDI:: NC_000016.10:1530254:C:T
Gene:: IFT140 (Varview), TMEM204 (Varview)
Functional Consequence:: 5_prime_UTR_variant,genic_downstream_transcript_variant,intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0./0 (KOREAN)
T=0.000015/4 (TOPMED)
T=0.000029/4 (GnomAD)
T=0.000071/1 (TOMMO)
HGVS:: NC_000016.10:g.1530255C>T, NC_000016.9:g.1580256C>T, NG_032783.1:g.86854G>A, XM_006720992.4:c.-1315G>A

Select item 149002942911.

rs1490029429 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 16:1538421 (GRCh38)
16:1588422 (GRCh37)
Canonical SPDI:: NC_000016.10:1538420:C:T
Gene:: IFT140 (Varview), TMEM204 (Varview)
Functional Consequence:: 3_prime_UTR_variant,genic_downstream_transcript_variant,intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000008/2 (TOPMED)
HGVS:: NC_000016.10:g.1538421C>T, NC_000016.9:g.1588422C>T, NG_032783.1:g.78688G>A, XM_011522772.4:c.*2305G>A, XM_011522772.3:c.*2305G>A, XM_011522772.2:c.*2305G>A, XM_011522772.1:c.*2305G>A, XM_047434976.1:c.*2305G>A, XM_047434972.1:c.*1244G>A

Select item 148997617112.

rs1489976171 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 16:1527629 (GRCh38)
16:1577630 (GRCh37)
Canonical SPDI:: NC_000016.10:1527628:T:C
Gene:: IFT140 (Varview), TMEM204 (Varview)
Functional Consequence:: 2KB_upstream_variant,genic_downstream_transcript_variant,intron_variant,upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
C=0.000004/1 (TOPMED)
HGVS:: NC_000016.10:g.1527629T>C, NC_000016.9:g.1577630T>C, NG_032783.1:g.89480A>G

Select item 148994111113.

rs1489941111 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 16:1554019 (GRCh38)
16:1604020 (GRCh37)
Canonical SPDI:: NC_000016.10:1554018:T:C
Gene:: IFT140 (Varview), TMEM204 (Varview)
Functional Consequence:: 3_prime_UTR_variant,genic_downstream_transcript_variant,intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000007/1 (GnomAD)
HGVS:: NC_000016.10:g.1554019T>C, NC_000016.9:g.1604020T>C, NG_032783.1:g.63090A>G, XM_005255726.5:c.*15A>G, XM_005255726.4:c.*15A>G, XM_005255726.3:c.*15A>G, XM_005255726.2:c.*15A>G, XM_005255726.1:c.*15A>G, XM_047434977.1:c.*15A>G, XM_047434978.1:c.*15A>G, XM_047434980.1:c.*15A>G, XM_047434979.1:c.*15A>G

Select item 148987786814.

rs1489877868 [Homo sapiens]

Variant type:: SNV
Alleles:: G>C [Show Flanks]
Chromosome:: 16:1550802 (GRCh38)
16:1600803 (GRCh37)
Canonical SPDI:: NC_000016.10:1550801:G:C
Gene:: IFT140 (Varview), TMEM204 (Varview)
Functional Consequence:: genic_downstream_transcript_variant,intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000007/1 (GnomAD)
C=0.000008/2 (TOPMED)
HGVS:: NC_000016.10:g.1550802G>C, NC_000016.9:g.1600803G>C, NG_032783.1:g.66307C>G

Select item 148980032415.

rs1489800324 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 16:1544176 (GRCh38)
16:1594177 (GRCh37)
Canonical SPDI:: NC_000016.10:1544175:C:T
Gene:: IFT140 (Varview), TMEM204 (Varview)
Functional Consequence:: genic_downstream_transcript_variant,intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000004/1 (TOPMED)
T=0.000007/1 (GnomAD)
T=0.000468/3 (1000Genomes)
HGVS:: NC_000016.10:g.1544176C>T, NC_000016.9:g.1594177C>T, NG_032783.1:g.72933G>A

Select item 148972460616.

rs1489724606 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 16:1549106 (GRCh38)
16:1599107 (GRCh37)
Canonical SPDI:: NC_000016.10:1549105:T:C
Gene:: IFT140 (Varview), TMEM204 (Varview)
Functional Consequence:: genic_downstream_transcript_variant,intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
C=0.000008/2 (TOPMED)
HGVS:: NC_000016.10:g.1549106T>C, NC_000016.9:g.1599107T>C, NG_032783.1:g.68003A>G

Select item 148961895517.

rs1489618955 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 16:1539633 (GRCh38)
16:1589634 (GRCh37)
Canonical SPDI:: NC_000016.10:1539632:T:C
Gene:: IFT140 (Varview), TMEM204 (Varview)
Functional Consequence:: 3_prime_UTR_variant,genic_downstream_transcript_variant,intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
C=0.000007/1 (GnomAD)
HGVS:: NC_000016.10:g.1539633T>C, NC_000016.9:g.1589634T>C, NG_032783.1:g.77476A>G, XM_011522772.4:c.*1093A>G, XM_011522772.3:c.*1093A>G, XM_011522772.2:c.*1093A>G, XM_011522772.1:c.*1093A>G, XM_047434976.1:c.*1093A>G, XM_047434972.1:c.*32A>G

Select item 148956981218.

rs1489569812 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 16:1548482 (GRCh38)
16:1598483 (GRCh37)
Canonical SPDI:: NC_000016.10:1548481:A:G
Gene:: IFT140 (Varview), TMEM204 (Varview)
Functional Consequence:: genic_downstream_transcript_variant,intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000007/1 (GnomAD)
G=0.000019/5 (TOPMED)
HGVS:: NC_000016.10:g.1548482A>G, NC_000016.9:g.1598483A>G, NG_032783.1:g.68627T>C

Select item 148929875419.

rs1489298754 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 16:1541863 (GRCh38)
16:1591864 (GRCh37)
Canonical SPDI:: NC_000016.10:1541862:G:A
Gene:: IFT140 (Varview), TMEM204 (Varview)
Functional Consequence:: genic_downstream_transcript_variant,intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000004/1 (TOPMED)
A=0.000007/1 (GnomAD)
HGVS:: NC_000016.10:g.1541863G>A, NC_000016.9:g.1591864G>A, NG_032783.1:g.75246C>T

Select item 148928225520.

rs1489282255 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 16:1530580 (GRCh38)
16:1580581 (GRCh37)
Canonical SPDI:: NC_000016.10:1530579:C:T
Gene:: IFT140 (Varview), TMEM204 (Varview)
Functional Consequence:: 5_prime_UTR_variant,genic_downstream_transcript_variant,intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000004/1 (TOPMED)
HGVS:: NC_000016.10:g.1530580C>T, NC_000016.9:g.1580581C>T, NG_032783.1:g.86529G>A, XM_006720992.4:c.-1640G>A

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