SNP Report

Basic Info

Name	rs2524005 dbSNP Ensembl
Location	chrCHR_HSCHR6_MHC_SSTO_CTG1:29923058 - 29923058(1)
Variant Alleles	G/A
Ancestral Allele	G
Minor Allele	A
Minor Allele Frequence	0.193291
Functional Annotation	downstream_gene_variant; upstream_gene_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000430151); upstream_gene_variant(ENST00000418981, ENST00000450128, ENST00000455932, ENST00000421242, ENST00000445948, ENST00000418780, ENST00000419369, ENST00000435665, ENST00000435780, ENST00000426349, ENST00000428321, ENST00000437770, ENST00000414908, ENST00000453494, ENST00000431463, ENST00000406611, ENST00000442622, ENST00000428988, ENST00000413313, ENST00000415983)
No. of Studies	1 (Positive: 0; Negative: 1; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 1)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Bergen, S. E.,2012		A	logistic regression: P-value > E-05 logistic regression: P-value > E-05	No significant association was observed in BD. No significant association was observed in BD.	Negative

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
HLA-K	major histocompatibility complex, class I, K (pseudogene)	6p21.3	Mapped by Literature SNP
HLA-U	major histocompatibility complex, class I, U (pseudogene)	6p21.3	Mapped by Literature SNP

SNPs in LD with rs2524005 (count: 43) View in gBrowse (chrCHR_HSCHR6_MHC_SSTO_CTG1:29794195..30095338 )

The LD data used here is based on HapMap rel#27. LD SNP pairs were selected with a threshold r²<=0.8.

Literature-origin SNPs (count: 0)

LD-proxies (count: 43)

rs_ID	Functional Annotation	r²[population]
rs1611630	downstream_gene_variant	0.881[CEU]
rs2844796	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]
rs2517866	upstream_gene_variant	0.85[CEU]
rs2517869	downstream_gene_variant	0.8[CEU]
rs9258636	upstream_gene_variant	0.834[CEU]
rs1611701		0.85[CEU]
rs6457149	downstream_gene_variant	1.0[CEU]
rs1611738		0.85[CEU]
rs1264807	downstream_gene_variant; upstream_gene_variant	0.945[CEU]
rs3132689		0.803[CEU]
rs2734983	upstream_gene_variant	0.812[CEU]
rs3129012	intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.8[CEU]
rs1108052	downstream_gene_variant; upstream_gene_variant	1.0[CEU]
rs1264702		1.0[CEU]
rs1655927	downstream_gene_variant; upstream_gene_variant	0.803[CEU]
rs2508049	upstream_gene_variant	0.85[CEU]
rs429511	intron_variant; non_coding_transcript_variant	0.85[CEU]
rs356971	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant; non_coding_transcript_exon_variant	0.85[CEU]
rs439935	downstream_gene_variant; upstream_gene_variant	0.85[CEU]
rs916569	downstream_gene_variant	1.0[CEU]
rs2517862	upstream_gene_variant	0.85[CEU]
rs2240071	3_prime_UTR_variant; downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.947[CEU]
rs1264697	downstream_gene_variant	1.0[CEU]
rs1611689		0.85[CEU]
rs2734970		0.85[CEU]
rs1116221	downstream_gene_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.86[CEU]
rs1264698	downstream_gene_variant	1.0[CEU]
rs1632926	downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.943[CEU]
rs1264703		1.0[CEU]
rs916570	downstream_gene_variant	0.86[CEU]
rs1116222	3_prime_UTR_variant; downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.86[CEU]
rs1110446	3_prime_UTR_variant; downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.949[CEU]
rs1264709		0.849[CEU]
rs1611714		0.85[CEU]
rs1611635	downstream_gene_variant	0.85[CEU]
rs356959	downstream_gene_variant; upstream_gene_variant	0.845[CEU]
rs1655900	downstream_gene_variant; 3_prime_UTR_variant	0.85[CEU]
rs2734986	downstream_gene_variant	0.848[CEU]
rs2517855	upstream_gene_variant	0.85[CEU]
rs1264695	downstream_gene_variant	1.0[CEU]
rs1611703		0.85[CEU]
rs1633005	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.85[CEU]
rs2248289	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]

Overlap with SZ from cross-disorder studies (count: 1)

Reference	Statistical Result	Description	Result Category
Bergen, S. E.,2012	logistic regression:for SZ full sample, OR=0.74, P-value = 3.81E-07	No significant association was observed in SZ.	Negative

Overlap with MDD from cross-disorder studies (count: 0)