Variant report

Variant	rs3781201
Chromosome Location	chr10:90095434-90095435
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:89620144..89622520-chr10:90093536..90095614,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10887807	0.97[ASN][1000 genomes]
rs11202703	0.91[ASN][1000 genomes]
rs11202705	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11202706	0.93[ASN][1000 genomes]
rs11202722	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11202726	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs11202731	0.90[ASN][1000 genomes]
rs11202734	0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs11528433	0.94[ASN][1000 genomes]
rs11598623	0.98[ASN][1000 genomes]
rs12217988	0.87[CHD][hapmap];0.81[JPT][hapmap]
rs12219687	0.84[ASN][1000 genomes]
rs12219831	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs12220632	0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs12221213	0.85[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12569922	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs12572813	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1426617	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1582223	0.84[ASN][1000 genomes]
rs1582224	0.87[CHD][hapmap];0.88[JPT][hapmap]
rs1613409	0.95[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs1648512	0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs1648523	0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs17111200	0.85[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1774970	0.81[JPT][hapmap]
rs1774971	0.95[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2195013	0.92[ASN][1000 genomes]
rs2241515	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3740279	0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs55749454	0.99[ASN][1000 genomes]
rs59513062	0.89[ASN][1000 genomes]
rs7075138	0.86[ASN][1000 genomes]
rs7086211	0.80[ASN][1000 genomes]
rs7097606	0.87[CHD][hapmap];0.81[JPT][hapmap]
rs74149704	0.97[ASN][1000 genomes]
rs74149714	0.82[ASN][1000 genomes]
rs74149715	0.82[ASN][1000 genomes]
rs752709	0.92[ASN][1000 genomes]
rs7919335	0.92[ASN][1000 genomes]
rs792224	0.85[ASN][1000 genomes]
rs792225	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs792227	0.90[ASN][1000 genomes]
rs792228	0.91[ASN][1000 genomes]
rs792229	0.85[ASN][1000 genomes]
rs792232	0.87[CHD][hapmap];0.88[JPT][hapmap]
rs880793	0.97[ASN][1000 genomes]
rs880794	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895879	chr10:90015725-90219298	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv551838	chr10:90058637-90137045	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv482385	chr10:90066140-90259751	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv948664	chr10:90076715-90517150	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3781201	ATAD1	cis	parietal	SCAN
rs3781201	CH25H	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90084600-90103600	Weak transcription	Ovary	ovary
2	chr10:90090000-90096600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr10:90093400-90095800	Weak transcription	GM12878-XiMat	blood
4	chr10:90093800-90095600	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr10:90093800-90095600	Weak transcription	Primary B cells from cord blood	blood
6	chr10:90094000-90095800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr10:90095400-90096800	Enhancers	Primary B cells from peripheral blood	blood

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