nstd157 (Frenkel et al. 2019)
- Organism:
- Human
- Study Type:
- Case-Set
- Submitter:
- Svetlana Frenkel
- Description:
- We aimed to examine changes in DNA copy number of a population-based cohort of persons with IBD and search for novel genetic risk factors for IBD. DNA samples from 243 individuals with IBD from the Manitoba IBD Cohort Study were analysed using SNP microarray technology to assess the prevalence of CNVs, such as chromosomal deletions or duplications in IBD. See Variant Summary counts for nstd157 in dbVar Variant Summary.
- Publication(s):
- Frenkel et al. 2019
Detailed Information: Download 1907 Variant Regions, Download 4402 Variant Calls, Download Both, FTP
Variant Summary
Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Submitted: GRCh37 (hg19)
| Sequence ID | Chr | Number of Variant Regions | Number of Variant Calls | Placement type | Link to graphical display |
|---|---|---|---|---|---|
| NC_000001.11 | Chr1 | 127 | 213 | Remapped | NC_000001.11 |
| NC_000002.12 | Chr2 | 124 | 317 | Remapped | NC_000002.12 |
| NC_000003.12 | Chr3 | 133 | 357 | Remapped | NC_000003.12 |
| NC_000004.12 | Chr4 | 106 | 263 | Remapped | NC_000004.12 |
| NC_000005.10 | Chr5 | 110 | 236 | Remapped | NC_000005.10 |
| NC_000006.12 | Chr6 | 120 | 252 | Remapped | NC_000006.12 |
| NC_000007.14 | Chr7 | 136 | 278 | Remapped | NC_000007.14 |
| NC_000008.11 | Chr8 | 106 | 245 | Remapped | NC_000008.11 |
| NC_000009.12 | Chr9 | 102 | 216 | Remapped | NC_000009.12 |
| NC_000010.11 | Chr10 | 80 | 164 | Remapped | NC_000010.11 |
| NC_000011.10 | Chr11 | 84 | 220 | Remapped | NC_000011.10 |
| NC_000012.12 | Chr12 | 90 | 243 | Remapped | NC_000012.12 |
| NC_000013.11 | Chr13 | 44 | 115 | Remapped | NC_000013.11 |
| NC_000014.9 | Chr14 | 61 | 205 | Remapped | NC_000014.9 |
| NC_000015.10 | Chr15 | 50 | 149 | Remapped | NC_000015.10 |
| NC_000016.10 | Chr16 | 117 | 211 | Remapped | NC_000016.10 |
| NC_000017.11 | Chr17 | 82 | 179 | Remapped | NC_000017.11 |
| NC_000018.10 | Chr18 | 29 | 113 | Remapped | NC_000018.10 |
| NC_000019.10 | Chr19 | 82 | 164 | Remapped | NC_000019.10 |
| NC_000020.11 | Chr20 | 55 | 106 | Remapped | NC_000020.11 |
| NC_000021.9 | Chr21 | 30 | 71 | Remapped | NC_000021.9 |
| NC_000022.11 | Chr22 | 32 | 60 | Remapped | NC_000022.11 |
| NT_187515.1 | Chr1|NT_187515.1 | 1 | 1 | Remapped | NT_187515.1 |
| NT_187516.1 | Chr1|NT_187516.1 | 1 | 18 | Remapped | NT_187516.1 |
| NW_009646195.1 | Chr1|NW_009646195.1 | 1 | 1 | Remapped | NW_009646195.1 |
| NW_011332688.1 | Chr1|NW_011332688.1 | 1 | 3 | Remapped | NW_011332688.1 |
| NW_012132914.1 | Chr1|NW_012132914.1 | 2 | 6 | Remapped | NW_012132914.1 |
| NW_018654706.1 | Chr1|NW_018654706.1 | 1 | 3 | Remapped | NW_018654706.1 |
| NT_187523.1 | Chr2|NT_187523.1 | 1 | 24 | Remapped | NT_187523.1 |
| NT_187530.1 | Chr2|NT_187530.1 | 1 | 1 | Remapped | NT_187530.1 |
| NT_187647.1 | Chr2|NT_187647.1 | 1 | 24 | Remapped | NT_187647.1 |
| NW_011332690.1 | Chr2|NW_011332690.1 | 1 | 1 | Remapped | NW_011332690.1 |
| NT_187678.1 | Chr3|NT_187678.1 | 5 | 26 | Remapped | NT_187678.1 |
| NT_187688.1 | Chr3|NT_187688.1 | 5 | 26 | Remapped | NT_187688.1 |
| NT_187689.1 | Chr3|NT_187689.1 | 5 | 26 | Remapped | NT_187689.1 |
| NT_187690.1 | Chr3|NT_187690.1 | 5 | 26 | Remapped | NT_187690.1 |
| NT_187691.1 | Chr3|NT_187691.1 | 5 | 26 | Remapped | NT_187691.1 |
| NT_187532.1 | Chr3|NT_187532.1 | 5 | 26 | Remapped | NT_187532.1 |
| NT_187649.1 | Chr3|NT_187649.1 | 5 | 26 | Remapped | NT_187649.1 |
| NW_019805488.1 | Chr3|NW_019805488.1 | 1 | 4 | Remapped | NW_019805488.1 |
| NT_187679.1 | Chr4|NT_187679.1 | 2 | 4 | Remapped | NT_187679.1 |
| NT_187543.1 | Chr4|NT_187543.1 | 1 | 3 | Remapped | NT_187543.1 |
| NT_187650.1 | Chr4|NT_187650.1 | 1 | 3 | Remapped | NT_187650.1 |
| NT_187546.1 | Chr5|NT_187546.1 | 1 | 6 | Remapped | NT_187546.1 |
| NT_187651.1 | Chr5|NT_187651.1 | 1 | 1 | Remapped | NT_187651.1 |
| NT_187652.1 | Chr5|NT_187652.1 | 1 | 6 | Remapped | NT_187652.1 |
| NW_003315917.2 | Chr5|NW_003315917.2 | 3 | 3 | Remapped | NW_003315917.2 |
| NW_003315919.1 | Chr5|NW_003315919.1 | 1 | 1 | Remapped | NW_003315919.1 |
| NW_003315920.1 | Chr5|NW_003315920.1 | 1 | 1 | Remapped | NW_003315920.1 |
| NW_016107298.1 | Chr5|NW_016107298.1 | 1 | 1 | Remapped | NW_016107298.1 |
| NT_187553.1 | Chr6|NT_187553.1 | 1 | 1 | Remapped | NT_187553.1 |
| NW_018654713.1 | Chr6|NW_018654713.1 | 2 | 3 | Remapped | NW_018654713.1 |
| NW_018654714.1 | Chr7|NW_018654714.1 | 1 | 1 | Remapped | NW_018654714.1 |
| NW_019805493.1 | Chr7|NW_019805493.1 | 1 | 1 | Remapped | NW_019805493.1 |
| NT_187567.1 | Chr8|NT_187567.1 | 1 | 1 | Remapped | NT_187567.1 |
| NT_187571.1 | Chr8|NT_187571.1 | 2 | 2 | Remapped | NT_187571.1 |
| NT_187576.1 | Chr8|NT_187576.1 | 6 | 8 | Remapped | NT_187576.1 |
| NW_018654716.1 | Chr8|NW_018654716.1 | 2 | 2 | Remapped | NW_018654716.1 |
| NW_018654717.1 | Chr8|NW_018654717.1 | 5 | 15 | Remapped | NW_018654717.1 |
| NW_009646201.1 | Chr9|NW_009646201.1 | 1 | 3 | Remapped | NW_009646201.1 |
| NW_003315934.1 | Chr10|NW_003315934.1 | 1 | 5 | Remapped | NW_003315934.1 |
| NW_013171806.1 | Chr10|NW_013171806.1 | 1 | 2 | Remapped | NW_013171806.1 |
| NT_187585.1 | Chr11|NT_187585.1 | 1 | 1 | Remapped | NT_187585.1 |
| NT_187586.1 | Chr11|NT_187586.1 | 3 | 3 | Remapped | NT_187586.1 |
| NW_015148966.1 | Chr11|NW_015148966.1 | 1 | 1 | Remapped | NW_015148966.1 |
| NT_187658.1 | Chr12|NT_187658.1 | 1 | 1 | Remapped | NT_187658.1 |
| NT_187587.1 | Chr12|NT_187587.1 | 4 | 19 | Remapped | NT_187587.1 |
| NW_011332696.1 | Chr12|NW_011332696.1 | 1 | 15 | Remapped | NW_011332696.1 |
| NW_015148967.1 | Chr12|NW_015148967.1 | 1 | 3 | Remapped | NW_015148967.1 |
| NW_018654718.1 | Chr12|NW_018654718.1 | 1 | 25 | Remapped | NW_018654718.1 |
| NW_019805499.1 | Chr12|NW_019805499.1 | 1 | 1 | Remapped | NW_019805499.1 |
| NW_011332698.1 | Chr13|NW_011332698.1 | 1 | 1 | Remapped | NW_011332698.1 |
| NT_187660.1 | Chr15|NT_187660.1 | 2 | 2 | Remapped | NT_187660.1 |
| NW_011332701.1 | Chr15|NW_011332701.1 | 2 | 2 | Remapped | NW_011332701.1 |
| NT_187383.1 | Chr16|NT_187383.1 | 1 | 1 | Remapped | NT_187383.1 |
| NT_187607.1 | Chr16|NT_187607.1 | 3 | 3 | Remapped | NT_187607.1 |
| NT_187608.1 | Chr16|NT_187608.1 | 5 | 5 | Remapped | NT_187608.1 |
| NW_017852933.1 | Chr16|NW_017852933.1 | 3 | 4 | Remapped | NW_017852933.1 |
| NT_187661.1 | Chr17|NT_187661.1 | 2 | 45 | Remapped | NT_187661.1 |
| NT_187662.1 | Chr17|NT_187662.1 | 1 | 1 | Remapped | NT_187662.1 |
| NT_187663.1 | Chr17|NT_187663.1 | 20 | 32 | Remapped | NT_187663.1 |
| NT_187611.1 | Chr17|NT_187611.1 | 2 | 2 | Remapped | NT_187611.1 |
| NT_187614.1 | Chr17|NT_187614.1 | 3 | 46 | Remapped | NT_187614.1 |
| NW_003315952.3 | Chr17|NW_003315952.3 | 1 | 1 | Remapped | NW_003315952.3 |
| NW_003315955.1 | Chr17|NW_003315955.1 | 1 | 5 | Remapped | NW_003315955.1 |
| NW_003871091.1 | Chr17|NW_003871091.1 | 1 | 5 | Remapped | NW_003871091.1 |
| NW_019805503.1 | Chr18|NW_019805503.1 | 1 | 1 | Remapped | NW_019805503.1 |
| NT_187693.1 | Chr19|NT_187693.1 | 5 | 20 | Remapped | NT_187693.1 |
| NW_003571061.2 | Chr19|NW_003571061.2 | 2 | 2 | Remapped | NW_003571061.2 |
| NW_003571060.1 | Chr19|NW_003571060.1 | 5 | 20 | Remapped | NW_003571060.1 |
| NW_003315962.1 | Chr19|NW_003315962.1 | 2 | 2 | Remapped | NW_003315962.1 |
| NW_003315964.2 | Chr19|NW_003315964.2 | 1 | 1 | Remapped | NW_003315964.2 |
| NW_003571054.1 | Chr19|NW_003571054.1 | 5 | 20 | Remapped | NW_003571054.1 |
| NT_187624.1 | Chr20|NT_187624.1 | 1 | 1 | Remapped | NT_187624.1 |
| NT_187631.1 | Chr22|NT_187631.1 | 1 | 1 | Remapped | NT_187631.1 |
| Sequence ID | Chr | Number of Variant Regions | Number of Variant Calls | Placement type | Link to graphical display |
|---|---|---|---|---|---|
| NC_000001.10 | Chr1 | 128 | 214 | Submitted | NC_000001.10 |
| NC_000002.11 | Chr2 | 124 | 317 | Submitted | NC_000002.11 |
| NC_000003.11 | Chr3 | 133 | 357 | Submitted | NC_000003.11 |
| NC_000004.11 | Chr4 | 106 | 263 | Submitted | NC_000004.11 |
| NC_000005.9 | Chr5 | 110 | 236 | Submitted | NC_000005.9 |
| NC_000006.11 | Chr6 | 120 | 252 | Submitted | NC_000006.11 |
| NC_000007.13 | Chr7 | 138 | 280 | Submitted | NC_000007.13 |
| NC_000008.10 | Chr8 | 106 | 245 | Submitted | NC_000008.10 |
| NC_000009.11 | Chr9 | 103 | 217 | Submitted | NC_000009.11 |
| NC_000010.10 | Chr10 | 81 | 168 | Submitted | NC_000010.10 |
| NC_000011.9 | Chr11 | 85 | 221 | Submitted | NC_000011.9 |
| NC_000012.11 | Chr12 | 90 | 243 | Submitted | NC_000012.11 |
| NC_000013.10 | Chr13 | 44 | 115 | Submitted | NC_000013.10 |
| NC_000014.8 | Chr14 | 61 | 205 | Submitted | NC_000014.8 |
| NC_000015.9 | Chr15 | 50 | 149 | Submitted | NC_000015.9 |
| NC_000016.9 | Chr16 | 117 | 211 | Submitted | NC_000016.9 |
| NC_000017.10 | Chr17 | 82 | 179 | Submitted | NC_000017.10 |
| NC_000018.9 | Chr18 | 29 | 113 | Submitted | NC_000018.9 |
| NC_000019.9 | Chr19 | 82 | 164 | Submitted | NC_000019.9 |
| NC_000020.10 | Chr20 | 56 | 122 | Submitted | NC_000020.10 |
| NC_000021.8 | Chr21 | 30 | 71 | Submitted | NC_000021.8 |
| NC_000022.10 | Chr22 | 32 | 60 | Submitted | NC_000022.10 |
| Variant Region remap status | Variant Call remap status | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Sequence ID | Chr | Variant Regions on source | Perfect | Good | Pass | Fail | Mult | Variant Calls on source | Perfect | Good | Pass | Fail | Mult |
| NC_000001.10 | Chr1 | 128 | 114 | 6 | 0 | 1 | 7 | 214 | 170 | 11 | 0 | 1 | 32 |
| NC_000002.11 | Chr2 | 124 | 116 | 1 | 4 | 0 | 3 | 317 | 271 | 2 | 18 | 0 | 26 |
| NC_000003.11 | Chr3 | 133 | 125 | 2 | 0 | 0 | 6 | 357 | 323 | 4 | 0 | 0 | 30 |
| NC_000004.11 | Chr4 | 106 | 100 | 3 | 1 | 0 | 2 | 263 | 253 | 5 | 1 | 0 | 4 |
| NC_000005.9 | Chr5 | 110 | 102 | 1 | 0 | 0 | 7 | 236 | 222 | 2 | 0 | 0 | 12 |
| NC_000006.11 | Chr6 | 120 | 115 | 2 | 0 | 0 | 3 | 252 | 246 | 2 | 0 | 0 | 4 |
| NC_000007.13 | Chr7 | 138 | 124 | 8 | 3 | 1 | 2 | 280 | 243 | 25 | 9 | 1 | 2 |
| NC_000008.10 | Chr8 | 106 | 83 | 7 | 0 | 0 | 16 | 245 | 210 | 7 | 0 | 0 | 28 |
| NC_000009.11 | Chr9 | 103 | 98 | 3 | 0 | 1 | 1 | 217 | 210 | 3 | 0 | 1 | 3 |
| NC_000010.10 | Chr10 | 81 | 72 | 0 | 6 | 1 | 2 | 168 | 150 | 0 | 7 | 4 | 7 |
| NC_000011.9 | Chr11 | 85 | 75 | 4 | 0 | 1 | 5 | 221 | 211 | 4 | 0 | 1 | 5 |
| NC_000012.11 | Chr12 | 90 | 81 | 0 | 0 | 0 | 9 | 243 | 179 | 0 | 0 | 0 | 64 |
| NC_000013.10 | Chr13 | 44 | 42 | 0 | 1 | 0 | 1 | 115 | 113 | 0 | 1 | 0 | 1 |
| NC_000014.8 | Chr14 | 61 | 58 | 2 | 1 | 0 | 0 | 205 | 202 | 2 | 1 | 0 | 0 |
| NC_000015.9 | Chr15 | 50 | 48 | 0 | 0 | 0 | 2 | 149 | 147 | 0 | 0 | 0 | 2 |
| NC_000016.9 | Chr16 | 117 | 103 | 1 | 2 | 0 | 11 | 211 | 192 | 5 | 2 | 0 | 12 |
| NC_000017.10 | Chr17 | 82 | 53 | 1 | 0 | 0 | 28 | 179 | 87 | 1 | 0 | 0 | 91 |
| NC_000018.9 | Chr18 | 29 | 27 | 1 | 0 | 0 | 1 | 113 | 111 | 1 | 0 | 0 | 1 |
| NC_000019.9 | Chr19 | 82 | 69 | 3 | 2 | 0 | 8 | 164 | 136 | 3 | 2 | 0 | 23 |
| NC_000020.10 | Chr20 | 56 | 47 | 7 | 0 | 1 | 1 | 122 | 97 | 8 | 0 | 16 | 1 |
| NC_000021.8 | Chr21 | 30 | 28 | 2 | 0 | 0 | 0 | 71 | 69 | 2 | 0 | 0 | 0 |
| NC_000022.10 | Chr22 | 32 | 29 | 2 | 0 | 0 | 1 | 60 | 57 | 2 | 0 | 0 | 1 |
Samplesets
Number of Samplesets: 1
- Size:
- 243
- Organisms:
- Homo sapiens
- Sampleset Phenotype(s):
- Inflammation of the large intestine
Experimental Details
| Experiment ID | Type | Method | Analysis | Number of Variant Calls |
|---|---|---|---|---|
| 1 | Discovery | SNP array | SNP genotyping analysis | 4,402 |