{{Rsnum
|rsid=3129934
|Gene=C6orf10
|Chromosome=6
|position=32368410
|Orientation=plus
|GMAF=0.1428
|Assembly=GRCh38
|GenomeBuild=38.1
|dbSNPBuild=141
|geno1=(C;C)
|geno2=(C;T)
|geno3=(T;T)
|Gene_s=C6orf10
}}{{ population diversity
| geno1=(C;C)
| geno2=(C;T)
| geno3=(T;T)
| CEU | 66.1 | 28.6 | 5.4
| HCB | 88.3 | 10.2 | 1.5
| JPT | 99.1 | 0.9 | 0.0
| YRI | 55.9 | 37.9 | 6.2
| ASW | 68.4 | 28.1 | 3.5
| CHB | 88.3 | 10.2 | 1.5
| CHD | 76.1 | 22.0 | 1.8
| GIH | 89.0 | 10.0 | 1.0
| LWK | 60.9 | 38.2 | 0.9
| MEX | 74.1 | 22.4 | 3.4
| MKK | 56.4 | 37.8 | 5.8
| TSI | 77.5 | 22.5 | 0.0
| HapMapRevision=28
}}[[rs3129934]] is a SNP near the HLA-class II region that may be associated with several autoimmune diseases.

In a study of two cohorts (Spanish and American [[multiple sclerosis]] patients, each numbering several hundred), [[rs3129934]] was the SNP most associated with increased risk for [[multiple sclerosis]]. The odds ratio was 3.3 (CI: 2.3 - 4.9, p = 9 x 10e-11). Seven other SNPs were also identified in this study as associated with increased risk for MS.{{PMID|18941528|OA=1
}}

{{PMID|17554260|OA=1
}} associated with [[type-1 diabetes]]. 1.6x risk of [[type-1 diabetes]]?

[[23andMe]] uses [[rs9273363]] instead of [[rs3129934]] in its reports on [[type 1 diabetes]] risk. This SNP was formerly used as a proxy for [[rs9272346]], with this explanation:
"Note: the 2007 Wellcome Trust paper reported a strong association between type 1 diabetes and the SNP rs9272346. Our quality control process flagged data for rs9272346 as unreliable, so we instead included the SNP rs3129934, which is also highly associated with type 1 diabetes. Both are in the HLA region, although the exact linkage patterns between tagging SNPs and traditionally determined HLA haplotypes is still being worked out."
However it is apparent that the HapMap frequencies for these two snps are very different.

[[rs9291683]], [[rs3129934]] and [[rs2705293]] discussed in the context of [[CNV]]s in a [https://sites.google.com/a/codushlaine.com/colm-o-dushlaine/23andcolm/day14-cnvs blog post]

{{PharmGKB
|RSID=rs3129934
|Name_s=
|Gene_s=C6orf10
|Feature=
|Evidence=PubMed ID:18941528; Web Resource:http://www.genome.gov/gwastudies/
|Annotation=GWAS results: Identification of a novel risk locus for multiple sclerosis at 13q31.3 by a pooled genome-wide scan of 500,000 single nucleotide polymorphisms. (Initial Sample Size: 242 cases, 242 controls; Replication Sample Size: 375 cases, 375 controls); (Region: 6p21.32; Reported Gene(s): HLA-DRB1; Risk Allele: rs3129934-T); (p-value= 0.00000000009).This variant is associated with Multiple sclerosis.
|Drugs=
|Drug Classes=
|Diseases=Multiple Sclerosis
|Curation Level=Non-Curated
|PharmGKB Accession ID=PA164740797
}}

{{PMID Auto
|PMID=22457343
|Title=A genome-wide association study in progressive multiple sclerosis
}}

{{PMID Auto
|PMID=17660530
|Title=Risk alleles for multiple sclerosis identified by a genomewide study.
}}

{{PMID Auto
|PMID=18252225
|Title=On the use of general control samples for genome-wide association studies: genetic matching highlights causal variants.
|OA=1
}}

{{PMID Auto
|PMID=20369022
|Title=Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations.
|OA=1
}}

{{PMID Auto
|PMID=20405052
|Title=The effect of single nucleotide polymorphisms from genome wide association studies in multiple sclerosis on gene expression.
|OA=1
}}

{{PMID Auto
|PMID=20546594
|Title=An application of Random Forests to a genome-wide association dataset: methodological considerations & new findings.
|OA=1
}}

{{GET Evidence
|impact=pathogenic
|qualified_impact=Insufficiently evaluated pathogenic
|inheritance=unknown
|quality_scores=Array
|dbsnp_id=rs3129934
|overall_frequency_n=101
|overall_frequency_d=124
|overall_frequency=0.814516
|n_genomes=49
|n_genomes_annotated=0
|n_haplomes=84
|n_articles=0
|n_articles_annotated=0
|in_gwas=Y
|in_pharmgkb=Y
|autoscore=2
|webscore=N
}}

{{on chip | 23andMe v1}}
{{on chip | 23andMe v2}}
{{on chip | 23andMe v3}}
{{on chip | 23andMe v4}}
{{on chip | Affy GenomeWide 6}}
{{on chip | HumanOmni1Quad}}
{{on chip | Illumina Human 1M}}