SNP Report

Basic Info

Name	rs138864 dbSNP Ensembl
Location	chr22:49811064 - 49811064(1)
Variant Alleles	G/A
Ancestral Allele	A
Minor Allele	A
Minor Allele Frequence	0.381989
Functional Annotation	downstream_gene_variant; intron_variant; NMD_transcript_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000624882); intron_variant(ENST00000216267, ENST00000404034, ENST00000404760, ENST00000438393, ENST00000457780); NMD_transcript_variant(ENST00000438393)
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
Nyegaard, M., 2010	G/A			None of the 11 Sequenom SNPs showed association with BPD. None of the 11 Sequenom SNPs showed association with BPD.	Negative

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
BRD1	bromodomain containing 1	22q13.33	2(2/0/0)

SNPs in LD with rs138864 (count: 40) View in gBrowse (chr22:49786849..49927975 )

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: 40)

rs_ID	Functional Annotation	r²[population]
rs7287579	downstream_gene_variant	0.939[CEU]
rs11703411	intron_variant	0.832[CEU]
rs7410537	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.939[CEU]
rs8135963	downstream_gene_variant; NMD_transcript_variant; synonymous_variant	0.939[CEU]
rs138866	intron_variant; NMD_transcript_variant; upstream_gene_variant	1.0[CEU]
rs138834	intron_variant; NMD_transcript_variant	0.814[CEU]
rs9616217	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.939[CEU]
rs4574208	intron_variant	0.937[CEU]
rs1569954	downstream_gene_variant; upstream_gene_variant	0.942[CEU]
rs138867	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	1.0[CEU]
rs138891	intron_variant; non_coding_transcript_variant	1.0[CEU]
rs4824111	downstream_gene_variant	0.942[CEU]
rs5770742	intron_variant	0.941[CEU]
rs5770741	intron_variant	0.939[CEU]
rs7511620	intron_variant; upstream_gene_variant	0.939[CEU]
rs138897	non_coding_transcript_exon_variant; non_coding_transcript_variant	1.0[CEU]
rs7410318	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.939[CEU]
rs9616367	intron_variant; NMD_transcript_variant; upstream_gene_variant	0.942[CEU]
rs4597652	intron_variant	0.819[CEU]
rs761879	downstream_gene_variant; upstream_gene_variant	0.939[CEU]
rs9616204	intron_variant; NMD_transcript_variant; upstream_gene_variant	0.936[CEU]
rs6520066	3_prime_UTR_variant; downstream_gene_variant; upstream_gene_variant	0.939[CEU]
rs910800	synonymous_variant	0.939[CEU]
rs138870	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	1.0[CEU]
rs9616388	non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant; upstream_gene_variant	0.939[CEU]
rs8139758	intron_variant	0.942[CEU]
rs5770739	intron_variant	0.941[CEU]
rs738711	3_prime_UTR_variant	0.942[CEU]
rs1321	3_prime_UTR_variant; downstream_gene_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.939[CEU]
rs5770728	intron_variant	0.876[CEU]
rs4824110	intron_variant	0.942[CEU]
rs5769762	intron_variant	0.942[CEU]
rs1033665	intron_variant	0.939[CEU]
rs9616380	intron_variant; upstream_gene_variant	0.939[CEU]
rs9627789	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.812[CEU]
rs5769760	intron_variant	0.822[CEU]
rs2236139	intron_variant	0.942[CEU]
rs2092982	3_prime_UTR_variant	0.939[CEU]
rs9616370	intron_variant; upstream_gene_variant	0.939[CEU]
rs138861	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.938[CEU]

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

Reference	Statistical Result	Description	Result Category
Nyegaard, M., 2010	P-value = 0.64, OR=1.06 in UK/DK sample	Nominal significant association with SZ	Positive

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