SNP Report

Basic Info

Name	rs138880 dbSNP Ensembl
Location	chr22:49824963 - 49824963(1)
Variant Alleles	A/C
Ancestral Allele	C
Minor Allele	C
Minor Allele Frequence	0.394369
Functional Annotation	intron_variant; upstream_gene_variant.
Consequence to Transcript	intron_variant(ENST00000404034, ENST00000404760); upstream_gene_variant(ENST00000216267, ENST00000438393, ENST00000457780, ENST00000459821, ENST00000494833)
No. of Studies	3 (Positive: 1; Negative: 2; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 3)

Reference	Allele Change	Statistical Values	Author Comments	Result Category
Severinsen, J. E., 2006 (b)	A/C	P-value = 0.0274 in BD, P-value = 0.0046 in BD and SZ P-value = 0.0274 in BD, P-value = 0.0046 in BD and SZ	Significant single-marker associations were observed for two...... Significant single-marker associations were observed for two BRD1 SNPs. More...	Positive
Yosifova, A.,2009	A/C	Allelic association: P-value = 0.38 Allelic association: P-value = 0.38	No significant association was observed No significant association was observed	Negative
Nyegaard, M., 2010	A/C		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 rs138880 (count: 43) View in gBrowse (chr22:49784434..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: 43)

rs_ID	Functional Annotation	r²[population]
rs6520066	3_prime_UTR_variant; downstream_gene_variant; upstream_gene_variant	0.939[CEU]; 0.881[TSI]
rs4824111	downstream_gene_variant	0.939[CEU]
rs138866	intron_variant; NMD_transcript_variant; upstream_gene_variant	1.0[CEU]; 0.911[TSI]
rs138861	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.935[CEU]
rs138867	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	1.0[CEU]; 0.97[TSI]
rs8139758	intron_variant	0.939[CEU]
rs761879	downstream_gene_variant; upstream_gene_variant	0.939[CEU]; 0.97[TSI]
rs4574208	intron_variant	0.934[CEU]
rs138832	intron_variant; NMD_transcript_variant	0.911[TSI]
rs1569954	downstream_gene_variant; upstream_gene_variant	0.939[CEU]
rs5770728	intron_variant	0.869[CEU]
rs9627789	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.812[CEU]
rs138897	non_coding_transcript_exon_variant; non_coding_transcript_variant	1.0[CEU]; 1.0[TSI]
rs7410537	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.939[CEU]; 0.822[TSI]
rs5770739	intron_variant	0.938[CEU]
rs9616367	intron_variant; NMD_transcript_variant; upstream_gene_variant	0.939[CEU]
rs7287579	downstream_gene_variant	0.939[CEU]
rs138834	intron_variant; NMD_transcript_variant	0.804[CEU]
rs1033665	intron_variant	0.939[CEU]; 0.858[TSI]
rs910800	synonymous_variant	0.939[CEU]; 0.91[TSI]
rs5770741	intron_variant	0.939[CEU]; 0.91[TSI]
rs138843	intron_variant; NMD_transcript_variant	0.881[TSI]
rs138870	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	1.0[CEU]
rs138891	intron_variant; non_coding_transcript_variant	1.0[CEU]
rs9616370	intron_variant; upstream_gene_variant	0.939[CEU]; 0.822[TSI]
rs5770742	intron_variant	0.938[CEU]
rs1321	3_prime_UTR_variant; downstream_gene_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.939[CEU]; 0.881[TSI]
rs11703411	intron_variant	0.832[CEU]; 0.858[TSI]
rs138850	intron_variant; NMD_transcript_variant	0.881[TSI]
rs7511620	intron_variant; upstream_gene_variant	0.939[CEU]; 0.822[TSI]
rs5769762	intron_variant	0.939[CEU]
rs2236139	intron_variant	0.939[CEU]
rs9616217	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.939[CEU]; 0.851[TSI]
rs738711	3_prime_UTR_variant	0.939[CEU]
rs9616380	intron_variant; upstream_gene_variant	0.939[CEU]; 0.822[TSI]
rs2092982	3_prime_UTR_variant	0.939[CEU]; 0.91[TSI]
rs4597652	intron_variant	0.819[CEU]
rs7410318	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.939[CEU]; 0.822[TSI]
rs9616204	intron_variant; NMD_transcript_variant; upstream_gene_variant	0.936[CEU]; 0.851[TSI]
rs5769760	intron_variant	0.812[CEU]
rs9616388	non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant; upstream_gene_variant	0.939[CEU]; 0.822[TSI]
rs4824110	intron_variant	0.939[CEU]
rs8135963	downstream_gene_variant; NMD_transcript_variant; synonymous_variant	0.939[CEU]; 0.91[TSI]

Overlap with SZ from cross-disorder studies (count: 2)

Reference	Statistical Result	Description	Result Category
Nyegaard, M., 2010	P-value = 0.45, OR=1.09 in UK/DK sample	Nominal significant association with SZ	Positive
Severinsen, J. E., 2006 (b)	P-value = 0.0061 in SZ, P-value = 0.0046 in BD and SZ	The promoter SNP rs138880 showed association in SZ and the combined case group.	Positive

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