Variant report

Variant	rs1663157
Chromosome Location	chr10:116869924-116869925
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	chr10:116869478..116872129-chr10:116874892..116876661,2	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1010610	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10736240	0.82[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs10787554	0.81[EUR][1000 genomes]
rs10787555	0.92[CEU][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap]
rs10787557	1.00[CEU][hapmap]
rs10885649	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10885651	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885655	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885657	0.91[ASN][1000 genomes]
rs10885659	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs10885660	0.83[EUR][1000 genomes]
rs10885661	0.82[EUR][1000 genomes]
rs10885662	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10885664	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs10885669	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10885671	0.92[CEU][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap]
rs10885672	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10885673	0.92[CEU][hapmap]
rs10885675	0.92[CEU][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap]
rs10885676	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10885680	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10885681	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs10885683	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs11197066	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197071	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197072	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs11197084	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11197087	0.81[EUR][1000 genomes]
rs11197091	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11197093	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs11197094	0.80[EUR][1000 genomes]
rs11197103	0.81[EUR][1000 genomes]
rs11197107	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11197110	0.92[CEU][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs11197115	0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11197122	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs11197126	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs11197127	0.92[CEU][hapmap]
rs11197150	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12218100	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs12218477	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12355617	0.84[EUR][1000 genomes]
rs12357053	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs12358411	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12360503	0.90[ASN][1000 genomes]
rs12573443	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1264748	0.83[EUR][1000 genomes]
rs1264756	0.82[YRI][hapmap];0.93[EUR][1000 genomes]
rs1264763	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs1264765	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1264768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1264774	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs1264782	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264783	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264794	0.92[CEU][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap]
rs1264795	0.96[CEU][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs1264796	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs1264799	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264802	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1268459	0.83[EUR][1000 genomes]
rs1268460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1268916	0.89[EUR][1000 genomes]
rs1270442	0.89[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs1270654	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1537685	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17092908	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs17722681	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1899721	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2152148	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256046	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2265930	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs2484265	0.81[EUR][1000 genomes]
rs2492980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2492981	0.81[EUR][1000 genomes]
rs35120367	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35728982	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4752724	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs923907	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1039002	chr10:116643095-116879483	Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv2761634	chr10:116643095-116879495	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv1045654	chr10:116654574-116879483	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1043242	chr10:116655057-116883386	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv831998	chr10:116847998-116969618	Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1663157	ATRNL1	cis	Esophagus Muscularis	GTEx
rs1663157	ATRNL1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116854800-116870000	Weak transcription	Aorta	Aorta
2	chr10:116865800-116872200	Weak transcription	Brain Germinal Matrix	brain
3	chr10:116866000-116885200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr10:116869600-116877000	Weak transcription	Colon Smooth Muscle	Colon

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