Variant report

Variant	rs10520138
Chromosome Location	chr15:39911352-39911353
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:39909459..39912628-chr15:39921888..39923922,3	MCF-7	breast:
2	chr15:39876322..39882916-chr15:39908249..39913734,7	MCF-7	breast:
3	chr15:39911219..39913428-chr15:39914753..39916393,2	MCF-7	breast:
4	chr15:39892602..39894529-chr15:39910543..39912935,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150667	Chromatin interaction
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10152640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520137	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10520142	0.81[CEU][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs11070220	0.86[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs11070221	0.89[ASN][1000 genomes]
rs11070222	0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs11070223	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11070224	0.89[ASN][1000 genomes]
rs11070225	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1134485	0.80[CHB][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs1134486	0.85[ASN][1000 genomes]
rs11630406	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs11631820	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs11631824	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs11632879	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs11635103	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs11852591	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs11852649	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs11856971	0.81[CHB][hapmap]
rs11857819	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs12050804	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs12443011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12900583	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs12908846	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12912082	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs1478604	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1478605	0.94[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16969386	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs16969395	0.97[ASN][1000 genomes]
rs16969410	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs16969459	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs16969475	0.81[CHB][hapmap]
rs16969478	0.81[CHB][hapmap]
rs1876852	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1876853	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs1904209	0.86[ASN][1000 genomes]
rs2169830	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2228261	0.85[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2229364	0.85[ASN][1000 genomes]
rs2292305	0.85[CHB][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs2411310	0.87[EUR][1000 genomes]
rs2411313	0.81[CHB][hapmap]
rs2411314	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs2411315	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2412412	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2412413	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs2412415	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2412417	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2412418	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2412419	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2412420	0.89[ASN][1000 genomes]
rs2412421	0.83[ASN][1000 genomes]
rs2618162	0.94[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2618163	0.89[CEU][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2664139	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2664141	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2898686	0.81[CHB][hapmap]
rs2898687	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs2898688	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs3743125	0.81[CHB][hapmap];0.86[ASN][1000 genomes]
rs4319738	0.87[EUR][1000 genomes]
rs4319740	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4349120	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs4429263	0.81[EUR][1000 genomes]
rs4493017	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs4505280	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs4547308	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs4583211	0.82[JPT][hapmap]
rs56938133	0.89[ASN][1000 genomes]
rs66781090	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67239630	0.89[ASN][1000 genomes]
rs7162070	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs7162781	0.81[CHB][hapmap]
rs7167366	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7168755	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs7169574	0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs7170335	0.80[CHB][hapmap];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7170682	0.90[ASN][1000 genomes]
rs7176721	0.81[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7177324	0.92[ASN][1000 genomes]
rs7179293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7180675	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7183544	0.82[ASN][1000 genomes]
rs753598	0.83[ASN][1000 genomes]
rs753599	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs8029602	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs8032035	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs8034594	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8035354	0.83[EUR][1000 genomes]
rs8036376	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs8036633	0.85[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs8039035	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9302102	0.86[ASN][1000 genomes]
rs949646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs964424	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs970280	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9806365	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9806647	0.92[ASN][1000 genomes]
rs999393	0.81[CHB][hapmap];0.81[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	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1048628	chr15:39877498-39940104	Enhancers Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1502	chr15:39884314-39928968	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39904000-39913400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:39906600-39916000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr15:39908800-39911400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:39909200-39913400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr15:39909800-39913200	Weak transcription	HUVEC	blood vessel
6	chr15:39910600-39915400	Weak transcription	A549	lung
7	chr15:39910800-39916200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:39910800-39917400	Weak transcription	Small Intestine	intestine
9	chr15:39911000-39912000	Enhancers	HMEC	breast
10	chr15:39911000-39912000	Enhancers	NHEK	skin
11	chr15:39911000-39912800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:39911000-39913400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:39911000-39913400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:39911000-39916000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:39911000-39916200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:39911000-39916200	Weak transcription	Left Ventricle	heart
17	chr15:39911000-39916400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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