SNP Links for Gene (Select 94233) - SNP

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Select item 14913747891.

rs1491374789 [Homo sapiens]

Variant type:: DEL
Alleles:: CA>- [Show Flanks]
Chromosome:: 10:86656944 (GRCh38)
10:88416701 (GRCh37)
Canonical SPDI:: NC_000010.11:86656943:CA:
Gene:: OPN4 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: -=0.00008/1 (ALFA)
HGVS:: NC_000010.11:g.86656944_86656945del, NC_000010.10:g.88416701_88416702del

Select item 14913383292.

rs1491338329 [Homo sapiens]

Variant type:: DEL
Alleles:: AT>- [Show Flanks]
Chromosome:: 10:86664016 (GRCh38)
10:88423773 (GRCh37)
Canonical SPDI:: NC_000010.11:86664015:AT:
Gene:: OPN4 (Varview), LOC105378409 (Varview)
Functional Consequence:: 3_prime_UTR_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: -=0.042052/754 (ALFA)
-=0.000035/1 (TOMMO)
-=0.02/12 (NorthernSweden)
-=0.020612/103 (1000Genomes)
-=0.034546/9144 (TOPMED)
-=0.034714/1613 (GnomAD_exomes)
-=0.035058/4892 (GnomAD)
-=0.037763/79 (ExAC)
-=0.041802/155 (TWINSUK)
-=0.042084/42 (GoNL)
-=0.045148/174 (ALSPAC)
HGVS:: NC_000010.11:g.86664016_86664017del, NC_000010.10:g.88423773_88423774del, NG_008876.1:g.453_454del, XM_017016955.2:c.*25_*26del, XM_017016955.1:c.*25_*26del, XM_017016956.2:c.*25_*26del, XM_017016956.1:c.*25_*26del

Select item 14913036983.

rs1491303698 has merged into rs749185273 [Homo sapiens]

Variant type:: DELINS
Alleles:: ACACACACACAC>-,ACACAC,ACACACAC,ACACACACAC,ACACACACACACAC,ACACACACACACACAC [Show Flanks]
Chromosome:: 10:86654134 (GRCh38)
10:88413891 (GRCh37)
Canonical SPDI:: NC_000010.11:86654124:CACACACACACACACACACAC:CACACACAC,NC_000010.11:86654124:CACACACACACACACACACAC:CACACACACACACAC,NC_000010.11:86654124:CACACACACACACACACACAC:CACACACACACACACAC,NC_000010.11:86654124:CACACACACACACACACACAC:CACACACACACACACACAC,NC_000010.11:86654124:CACACACACACACACACACAC:CACACACACACACACACACACAC,NC_000010.11:86654124:CACACACACACACACACACAC:CACACACACACACACACACACACAC
Gene:: OPN4 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: CACACACACACACAC=0./0 (ALFA)
HGVS:: NC_000010.11:g.86654126AC[4], NC_000010.11:g.86654126AC[7], NC_000010.11:g.86654126AC[8], NC_000010.11:g.86654126AC[9], NC_000010.11:g.86654126AC[11], NC_000010.11:g.86654126AC[12], NC_000010.10:g.88413883AC[4], NC_000010.10:g.88413883AC[7], NC_000010.10:g.88413883AC[8], NC_000010.10:g.88413883AC[9], NC_000010.10:g.88413883AC[11], NC_000010.10:g.88413883AC[12]

Select item 14912980304.

rs1491298030 [Homo sapiens]

Variant type:: DELINS
Alleles:: CA>- [Show Flanks]
Chromosome:: 10:86654406 (GRCh38)
10:88414163 (GRCh37)
Canonical SPDI:: NC_000010.11:86654401:CACACA:CACA
Gene:: OPN4 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by cluster
MAF:: -=0.0008/3 (TWINSUK)
-=0.001/4 (ALSPAC)
HGVS:: NC_000010.11:g.86654402CA[2], NC_000010.10:g.88414159CA[2]

Select item 14910755065.

rs1491075506 has merged into rs763495636 [Homo sapiens]

Variant type:: DELINS
Alleles:: TC>-,TCTC [Show Flanks]
Chromosome:: 10:86654401 (GRCh38)
10:88414158 (GRCh37)
Canonical SPDI:: NC_000010.11:86654399:CTC:C,NC_000010.11:86654399:CTC:CTCTC
Gene:: OPN4 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: CTCTC=0./0 (ALFA)
CT=0.18393/682 (TWINSUK)
CT=0.18786/724 (ALSPAC)
HGVS:: NC_000010.11:g.86654401_86654402del, NC_000010.11:g.86654401_86654402dup, NC_000010.10:g.88414158_88414159del, NC_000010.10:g.88414158_88414159dup

Select item 14910673156.

rs1491067315 has merged into rs763495636 [Homo sapiens]

Variant type:: DELINS
Alleles:: TC>-,TCTC [Show Flanks]
Chromosome:: 10:86654401 (GRCh38)
10:88414158 (GRCh37)
Canonical SPDI:: NC_000010.11:86654399:CTC:C,NC_000010.11:86654399:CTC:CTCTC
Gene:: OPN4 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: CTCTC=0./0 (ALFA)
CT=0.18393/682 (TWINSUK)
CT=0.18786/724 (ALSPAC)
HGVS:: NC_000010.11:g.86654401_86654402del, NC_000010.11:g.86654401_86654402dup, NC_000010.10:g.88414158_88414159del, NC_000010.10:g.88414158_88414159dup

Select item 14909408357.

rs1490940835 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 10:86660709 (GRCh38)
10:88420466 (GRCh37)
Canonical SPDI:: NC_000010.11:86660708:G:A
Gene:: OPN4 (Varview), LOC105378409 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000011/3 (TOPMED)
HGVS:: NC_000010.11:g.86660709G>A, NC_000010.10:g.88420466G>A

Select item 14906817018.

rs1490681701 [Homo sapiens]

Variant type:: DEL
Alleles:: CT>- [Show Flanks]
Chromosome:: 10:86653784 (GRCh38)
10:88413541 (GRCh37)
Canonical SPDI:: NC_000010.11:86653783:CT:
Gene:: OPN4 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: -=0./0 (ALFA)
-=0.000004/1 (TOPMED)
HGVS:: NC_000010.11:g.86653784_86653785del, NC_000010.10:g.88413541_88413542del

Select item 14904436759.

rs1490443675 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 10:86660259 (GRCh38)
10:88420016 (GRCh37)
Canonical SPDI:: NC_000010.11:86660258:G:A
Gene:: OPN4 (Varview), LOC105378409 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000004/1 (TOPMED)
HGVS:: NC_000010.11:g.86660259G>A, NC_000010.10:g.88420016G>A

Select item 149023466710.

rs1490234667 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 10:86665769 (GRCh38)
10:88425526 (GRCh37)
Canonical SPDI:: NC_000010.11:86665768:C:T
Gene:: LDB3 (Varview), OPN4 (Varview), LOC105378409 (Varview)
Functional Consequence:: 3_prime_UTR_variant,2KB_upstream_variant,upstream_transcript_variant,intron_variant,genic_downstream_transcript_variant
Validated:: by frequency
MAF:: T=0.000004/1 (GnomAD_exomes)
HGVS:: NC_000010.11:g.86665769C>T, NC_000010.10:g.88425526C>T, NG_008876.1:g.2206C>T, NM_033282.4:c.*18C>T, NM_033282.3:c.*18C>T, NM_001030015.3:c.*18C>T, NM_001030015.2:c.*18C>T

Select item 149000822811.

rs1490008228 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 10:86658981 (GRCh38)
10:88418738 (GRCh37)
Canonical SPDI:: NC_000010.11:86658980:G:A
Gene:: OPN4 (Varview), LOC105378409 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000008/2 (TOPMED)
A=0.000035/1 (TOMMO)
HGVS:: NC_000010.11:g.86658981G>A, NC_000010.10:g.88418738G>A

Select item 148963976712.

rs1489639767 [Homo sapiens]

Variant type:: SNV
Alleles:: G>C [Show Flanks]
Chromosome:: 10:86665762 (GRCh38)
10:88425519 (GRCh37)
Canonical SPDI:: NC_000010.11:86665761:G:C
Gene:: LDB3 (Varview), OPN4 (Varview), LOC105378409 (Varview)
Functional Consequence:: 3_prime_UTR_variant,2KB_upstream_variant,upstream_transcript_variant,intron_variant,genic_downstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000004/1 (TOPMED)
C=0.000007/1 (GnomAD)
HGVS:: NC_000010.11:g.86665762G>C, NC_000010.10:g.88425519G>C, NG_008876.1:g.2199G>C, NM_033282.4:c.*11G>C, NM_033282.3:c.*11G>C, NM_001030015.3:c.*11G>C, NM_001030015.2:c.*11G>C

Select item 148944597713.

rs1489445977 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C,G [Show Flanks]
Chromosome:: 10:86653206 (GRCh38)
10:88412963 (GRCh37)
Canonical SPDI:: NC_000010.11:86653205:A:C,NC_000010.11:86653205:A:G
Gene:: OPN4 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
HGVS:: NC_000010.11:g.86653206A>C, NC_000010.11:g.86653206A>G, NC_000010.10:g.88412963A>C, NC_000010.10:g.88412963A>G

Select item 148929605114.

rs1489296051 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 10:86663740 (GRCh38)
10:88423497 (GRCh37)
Canonical SPDI:: NC_000010.11:86663739:G:A
Gene:: OPN4 (Varview), LOC105378409 (Varview)
Functional Consequence:: missense_variant,coding_sequence_variant,intron_variant
HGVS:: NC_000010.11:g.86663740G>A, NC_000010.10:g.88423497G>A, NG_008876.1:g.177G>A, NM_033282.4:c.1336G>A, NM_033282.3:c.1336G>A, NM_001030015.3:c.1369G>A, NM_001030015.2:c.1369G>A, XM_017016955.2:c.1369G>A, XM_017016955.1:c.1369G>A, XM_017016956.2:c.1336G>A, XM_017016956.1:c.1336G>A, NP_150598.1:p.Glu446Lys, NP_001025186.1:p.Glu457Lys, XP_016872444.1:p.Glu457Lys, XP_016872445.1:p.Glu446Lys

Select item 148865977015.

rs1488659770 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 10:86665418 (GRCh38)
10:88425175 (GRCh37)
Canonical SPDI:: NC_000010.11:86665417:A:G
Gene:: LDB3 (Varview), OPN4 (Varview), LOC105378409 (Varview)
Functional Consequence:: 2KB_upstream_variant,genic_downstream_transcript_variant,upstream_transcript_variant,intron_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
G=0.000004/1 (TOPMED)
HGVS:: NC_000010.11:g.86665418A>G, NC_000010.10:g.88425175A>G, NG_008876.1:g.1855A>G

Select item 148862392016.

rs1488623920 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 10:86652545 (GRCh38)
10:88412302 (GRCh37)
Canonical SPDI:: NC_000010.11:86652544:A:G
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
G=0.000004/1 (TOPMED)
HGVS:: NC_000010.11:g.86652545A>G, NC_000010.10:g.88412302A>G

Select item 148862007017.

rs1488620070 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 10:86656269 (GRCh38)
10:88416026 (GRCh37)
Canonical SPDI:: NC_000010.11:86656268:G:A
Gene:: OPN4 (Varview)
Functional Consequence:: missense_variant,coding_sequence_variant
Validated:: by frequency
MAF:: A=0.000004/1 (GnomAD_exomes)
HGVS:: NC_000010.11:g.86656269G>A, NC_000010.10:g.88416026G>A, NM_033282.4:c.259G>A, NM_033282.3:c.259G>A, NM_001030015.3:c.259G>A, NM_001030015.2:c.259G>A, XM_017016955.2:c.259G>A, XM_017016955.1:c.259G>A, XM_017016956.2:c.259G>A, XM_017016956.1:c.259G>A, NP_150598.1:p.Gly87Ser, NP_001025186.1:p.Gly87Ser, XP_016872444.1:p.Gly87Ser, XP_016872445.1:p.Gly87Ser

Select item 148846644418.

rs1488466444 [Homo sapiens]

Variant type:: SNV
Alleles:: A>T [Show Flanks]
Chromosome:: 10:86654049 (GRCh38)
10:88413806 (GRCh37)
Canonical SPDI:: NC_000010.11:86654048:A:T
Gene:: OPN4 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000008/1 (GnomAD)
T=0.000023/6 (TOPMED)
HGVS:: NC_000010.11:g.86654049A>T, NC_000010.10:g.88413806A>T

Select item 148826228119.

rs1488262281 [Homo sapiens]

Variant type:: SNV
Alleles:: G>C,T [Show Flanks]
Chromosome:: 10:86665391 (GRCh38)
10:88425148 (GRCh37)
Canonical SPDI:: NC_000010.11:86665390:G:C,NC_000010.11:86665390:G:T
Gene:: LDB3 (Varview), OPN4 (Varview), LOC105378409 (Varview)
Functional Consequence:: 2KB_upstream_variant,genic_downstream_transcript_variant,upstream_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000008/2 (TOPMED)
HGVS:: NC_000010.11:g.86665391G>C, NC_000010.11:g.86665391G>T, NC_000010.10:g.88425148G>C, NC_000010.10:g.88425148G>T, NG_008876.1:g.1828G>C, NG_008876.1:g.1828G>T

Select item 148816444820.

rs1488164448 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 10:86659122 (GRCh38)
10:88418879 (GRCh37)
Canonical SPDI:: NC_000010.11:86659121:G:A
Gene:: OPN4 (Varview), LOC105378409 (Varview)
Functional Consequence:: intron_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_000010.11:g.86659122G>A, NC_000010.10:g.88418879G>A

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