Variant report

Variant	rs6492909
Chromosome Location	chr15:39954026-39954027
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39870612..39877795-chr15:39952369..39962860,18	MCF-7	breast:
2	chr15:39945408..39946992-chr15:39953107..39955288,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 154 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:148)

rs_ID	r²[population]
rs1105159	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs11070220	0.80[CEU][hapmap]
rs11070221	0.82[EUR][1000 genomes]
rs11070222	0.82[EUR][1000 genomes]
rs11070223	0.83[EUR][1000 genomes]
rs11070224	0.82[EUR][1000 genomes]
rs11070225	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs11070226	0.91[EUR][1000 genomes]
rs11070227	0.91[EUR][1000 genomes]
rs11070228	0.91[EUR][1000 genomes]
rs11070231	0.85[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs11630406	0.80[CEU][hapmap];0.91[EUR][1000 genomes]
rs11631820	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs11631824	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs11632117	0.88[EUR][1000 genomes]
rs11632879	0.80[CEU][hapmap];0.88[EUR][1000 genomes]
rs11635103	0.80[CEU][hapmap];0.91[EUR][1000 genomes]
rs11636823	0.91[EUR][1000 genomes]
rs11638041	0.88[EUR][1000 genomes]
rs11638558	0.88[EUR][1000 genomes]
rs11852591	0.80[CEU][hapmap];0.91[EUR][1000 genomes]
rs11852649	0.80[CEU][hapmap];0.91[EUR][1000 genomes]
rs11855487	0.86[EUR][1000 genomes]
rs11856971	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs11857819	0.82[EUR][1000 genomes]
rs12050804	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs12899323	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12900024	0.85[ASN][1000 genomes]
rs12900583	0.94[CHB][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs12901142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903514	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908846	0.83[EUR][1000 genomes]
rs12911549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12911999	0.89[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs16969386	0.83[EUR][1000 genomes]
rs16969395	0.83[EUR][1000 genomes]
rs16969410	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs16969426	0.88[EUR][1000 genomes]
rs16969429	0.88[EUR][1000 genomes]
rs16969451	0.88[EUR][1000 genomes]
rs16969459	0.80[CEU][hapmap];0.88[EUR][1000 genomes]
rs16969475	0.91[EUR][1000 genomes]
rs16969478	0.91[EUR][1000 genomes]
rs172104	0.87[JPT][hapmap]
rs1876853	0.88[EUR][1000 genomes]
rs1906152	0.90[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs1906155	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1906156	0.90[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs1994379	0.95[CHB][hapmap]
rs2129459	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2411299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2411300	0.90[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2411301	0.90[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2411307	0.90[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2411308	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2411309	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2411310	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs2411311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2411312	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2411313	0.80[CEU][hapmap];0.91[EUR][1000 genomes]
rs2411314	0.91[EUR][1000 genomes]
rs2412413	0.88[EUR][1000 genomes]
rs2412414	0.88[EUR][1000 genomes]
rs2412415	0.80[CEU][hapmap];0.88[EUR][1000 genomes]
rs2412416	0.88[EUR][1000 genomes]
rs2412417	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs2412419	0.81[EUR][1000 genomes]
rs2412420	0.81[EUR][1000 genomes]
rs2631697	0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2631700	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2631701	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2631702	0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2631704	0.87[ASN][1000 genomes]
rs2631705	0.90[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2631710	0.85[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2664125	0.87[ASN][1000 genomes]
rs2664133	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2664135	0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs28437905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28581473	0.94[ASN][1000 genomes]
rs2898685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2898686	0.80[CEU][hapmap];0.87[EUR][1000 genomes]
rs2898688	0.80[CEU][hapmap];0.88[EUR][1000 genomes]
rs2898962	0.88[EUR][1000 genomes]
rs3103065	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs4319738	0.95[ASN][1000 genomes]
rs4349120	0.80[CEU][hapmap];0.88[EUR][1000 genomes]
rs4429263	0.90[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs4476148	0.89[ASN][1000 genomes]
rs4479205	0.86[EUR][1000 genomes]
rs4480779	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4493017	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs4505280	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs4526992	0.96[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4547308	0.80[CEU][hapmap];0.88[EUR][1000 genomes]
rs4572354	0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs4583211	0.93[EUR][1000 genomes]
rs4591113	0.90[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs4606692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4628934	0.88[EUR][1000 genomes]
rs4924376	0.89[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs4924377	0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs56938133	0.82[EUR][1000 genomes]
rs59449051	0.93[EUR][1000 genomes]
rs60164392	0.88[EUR][1000 genomes]
rs60195210	0.88[EUR][1000 genomes]
rs61130460	0.91[EUR][1000 genomes]
rs61439563	0.93[EUR][1000 genomes]
rs61568256	0.91[EUR][1000 genomes]
rs6492910	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6492911	0.95[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs67239630	0.81[EUR][1000 genomes]
rs68183224	0.84[ASN][1000 genomes]
rs7162070	0.88[EUR][1000 genomes]
rs7162781	0.91[EUR][1000 genomes]
rs7165067	0.80[CHB][hapmap]
rs7167100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167184	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7168755	0.80[CEU][hapmap];0.88[EUR][1000 genomes]
rs7169478	0.84[EUR][1000 genomes]
rs7169574	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs7177324	0.81[EUR][1000 genomes]
rs7177857	0.84[ASN][1000 genomes]
rs7179013	0.90[CHB][hapmap]
rs7179608	0.91[EUR][1000 genomes]
rs72725079	0.88[EUR][1000 genomes]
rs72725080	0.88[EUR][1000 genomes]
rs72725084	0.88[EUR][1000 genomes]
rs72725093	0.91[EUR][1000 genomes]
rs72725101	0.91[EUR][1000 genomes]
rs753599	0.80[CEU][hapmap]
rs8026916	0.88[EUR][1000 genomes]
rs8029602	0.91[EUR][1000 genomes]
rs8032035	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs8032289	0.88[EUR][1000 genomes]
rs8033902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034543	0.95[ASN][1000 genomes]
rs8034885	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8035354	0.94[ASN][1000 genomes]
rs8036226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042068	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs884584	0.93[EUR][1000 genomes]
rs9302102	0.82[EUR][1000 genomes]
rs937960	0.90[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs951358	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9672572	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9806647	0.81[EUR][1000 genomes]
rs999393	0.80[CEU][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39938000-39957600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:39944800-39955600	Weak transcription	Fetal Lung	lung
3	chr15:39948400-39956000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:39949400-39956200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:39950200-39957200	Weak transcription	HSMM	muscle
6	chr15:39950400-39955800	Weak transcription	Hela-S3	cervix
7	chr15:39950400-39957200	Weak transcription	HSMMtube	muscle
8	chr15:39950800-39957800	Weak transcription	HUVEC	blood vessel
9	chr15:39953400-39954400	Enhancers	Fetal Kidney	kidney
10	chr15:39953400-39954800	Enhancers	NHDF-Ad	bronchial
11	chr15:39953600-39954400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:39953800-39954200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:39953800-39954200	Enhancers	NHLF	lung
14	chr15:39953800-39954400	Enhancers	HMEC	breast
15	chr15:39953800-39954400	Enhancers	NH-A	brain
16	chr15:39953800-39954400	Enhancers	NHEK	skin
17	chr15:39953800-39954600	Enhancers	Muscle Satellite Cultured Cells	--
18	chr15:39954000-39954400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:39954000-39954400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:39954000-39954800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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