Variant report

Variant	rs1569476
Chromosome Location	chr1:169608917-169608918
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1011266	0.90[ASN][1000 genomes]
rs10919204	0.99[ASN][1000 genomes]
rs10919207	0.99[ASN][1000 genomes]
rs10919208	0.92[ASN][1000 genomes]
rs10919214	0.92[ASN][1000 genomes]
rs10919216	0.95[ASN][1000 genomes]
rs10919219	0.99[ASN][1000 genomes]
rs11487513	0.99[ASN][1000 genomes]
rs12067152	0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs12076747	0.99[ASN][1000 genomes]
rs12081319	0.99[ASN][1000 genomes]
rs12087424	0.99[ASN][1000 genomes]
rs12116948	0.95[ASN][1000 genomes]
rs12116974	0.93[ASN][1000 genomes]
rs12123695	0.99[ASN][1000 genomes]
rs12126695	0.97[ASN][1000 genomes]
rs12131631	0.99[ASN][1000 genomes]
rs12140128	0.93[ASN][1000 genomes]
rs1569474	0.93[ASN][1000 genomes]
rs1800805	0.92[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1800808	0.92[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs2235302	0.81[ASN][1000 genomes]
rs2236868	0.86[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.84[TSI][hapmap];0.87[ASN][1000 genomes]
rs28409897	0.99[ASN][1000 genomes]
rs3917655	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3917657	0.92[ASN][1000 genomes]
rs3917675	0.80[CHB][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs3917681	0.93[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs3917682	0.92[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3917702	0.90[ASN][1000 genomes]
rs3917709	0.87[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs3917729	0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs58647626	0.99[ASN][1000 genomes]
rs60035985	0.99[ASN][1000 genomes]
rs6131	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs66920835	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72712029	0.98[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv532586	chr1:169593222-169713184	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv159209	chr1:169607718-169613389	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Total ventricular volume	21116278	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1569476	C1orf112	cis	cerebellum	SCAN
rs1569476	C1orf156	cis	cerebellum	SCAN
rs1569476	C1orf156	cis	parietal	SCAN
rs1569476	SELL	cis	parietal	SCAN
rs1569476	FMO6P	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169605200-169617000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:169608600-169609000	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr1:169608600-169609200	Enhancers	Dnd41	blood
4	chr1:169608800-169609000	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr1:169608800-169609200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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