Variant report

Variant	rs2411315
Chromosome Location	chr15:39933475-39933476
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	chr15:39930109..39933577-chr15:39957965..39961029,3	MCF-7	breast:
2	chr15:39874737..39877413-chr15:39931788..39934836,3	MCF-7	breast:

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10152640	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10520137	0.82[CHB][hapmap]
rs10520138	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]
rs10520142	0.82[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11070222	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs11070223	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs11070225	0.83[CHB][hapmap]
rs11070226	0.89[ASN][1000 genomes]
rs11070227	0.89[ASN][1000 genomes]
rs11070228	0.89[ASN][1000 genomes]
rs11630406	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs11631820	0.86[CEU][hapmap];0.92[EUR][1000 genomes]
rs11631824	0.86[CEU][hapmap];0.92[EUR][1000 genomes]
rs11632117	0.92[ASN][1000 genomes]
rs11632879	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs11635103	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs11636823	0.92[ASN][1000 genomes]
rs11638041	0.89[ASN][1000 genomes]
rs11638558	0.89[ASN][1000 genomes]
rs11852591	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs11852649	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs11855487	0.89[ASN][1000 genomes]
rs11856971	0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs11857819	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs12050804	0.84[CEU][hapmap];0.91[EUR][1000 genomes]
rs12443011	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12900583	0.80[CEU][hapmap];0.90[EUR][1000 genomes]
rs12908846	0.82[CHB][hapmap]
rs1478604	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1478605	0.94[CEU][hapmap];0.80[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16969386	0.82[CHB][hapmap]
rs16969395	0.80[ASN][1000 genomes]
rs16969410	0.87[CHB][hapmap]
rs16969426	0.89[ASN][1000 genomes]
rs16969429	0.89[ASN][1000 genomes]
rs16969451	0.89[ASN][1000 genomes]
rs16969459	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs16969475	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs16969478	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1876852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1876853	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2169830	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2411310	0.83[YRI][hapmap];0.92[EUR][1000 genomes]
rs2411313	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2411314	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2412412	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412413	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2412414	0.89[ASN][1000 genomes]
rs2412415	0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2412416	0.89[ASN][1000 genomes]
rs2412417	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2412418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412419	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2618162	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2618163	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2664139	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2664141	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2898686	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2898687	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2898688	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2898962	0.89[ASN][1000 genomes]
rs4319738	0.92[EUR][1000 genomes]
rs4319740	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4349120	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs4429263	0.85[EUR][1000 genomes]
rs4479205	0.89[ASN][1000 genomes]
rs4493017	0.86[CEU][hapmap];0.84[YRI][hapmap];0.92[EUR][1000 genomes]
rs4505280	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs4526992	0.90[ASN][1000 genomes]
rs4547308	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs4583211	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4628934	0.89[ASN][1000 genomes]
rs59449051	0.91[ASN][1000 genomes]
rs60164392	0.89[ASN][1000 genomes]
rs60195210	0.89[ASN][1000 genomes]
rs61130460	0.90[ASN][1000 genomes]
rs61439563	0.90[ASN][1000 genomes]
rs61568256	0.90[ASN][1000 genomes]
rs66781090	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7162070	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs7162781	0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7167184	0.89[ASN][1000 genomes]
rs7167366	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7168755	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs7170335	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7176721	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7179293	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7179608	0.90[ASN][1000 genomes]
rs7180675	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72725079	0.89[ASN][1000 genomes]
rs72725080	0.89[ASN][1000 genomes]
rs72725084	0.89[ASN][1000 genomes]
rs72725093	0.91[ASN][1000 genomes]
rs72725101	0.91[ASN][1000 genomes]
rs8026916	0.89[ASN][1000 genomes]
rs8029602	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs8032035	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs8032289	0.89[ASN][1000 genomes]
rs8034594	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8035354	0.88[EUR][1000 genomes]
rs8039035	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs884584	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs949646	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs964424	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9806365	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs999393	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39916400-39937800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:39921400-39937600	Weak transcription	Psoas Muscle	Psoas
3	chr15:39923800-39939600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:39926400-39934400	Weak transcription	Pancreas	Pancrea
5	chr15:39930800-39933800	Enhancers	HepG2	liver
6	chr15:39931400-39935600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:39931400-39937000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr15:39932200-39934800	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr15:39932200-39935400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:39932600-39934800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:39932600-39935400	Enhancers	HMEC	breast
12	chr15:39932600-39935400	Enhancers	HUVEC	blood vessel
13	chr15:39932800-39933600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:39932800-39933800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr15:39932800-39933800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:39932800-39934000	Enhancers	Placenta Amnion	Placenta Amnion
17	chr15:39932800-39934800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr15:39932800-39935200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:39933000-39933600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:39933000-39934000	Flanking Active TSS	Hela-S3	cervix
21	chr15:39933000-39935200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr15:39933000-39935400	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr15:39933000-39936000	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr15:39933200-39933800	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr15:39933200-39934600	Weak transcription	Brain Anterior Caudate	brain
26	chr15:39933200-39935400	Enhancers	Colon Smooth Muscle	Colon
27	chr15:39933400-39933600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr15:39933400-39933600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr15:39933400-39933800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr15:39933400-39933800	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr15:39933400-39934000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr15:39933400-39934000	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr15:39933400-39934400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr15:39933400-39934400	Enhancers	Muscle Satellite Cultured Cells	--
35	chr15:39933400-39934800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr15:39933400-39934800	Flanking Active TSS	NHEK	skin
37	chr15:39933400-39935000	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr15:39933400-39935000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr15:39933400-39935200	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr15:39933400-39935400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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