Variant report

Variant	rs10015639
Chromosome Location	chr4:87891565-87891566
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87885535..87895894-chr4:87923652..87929924,15	K562	blood:
2	chr4:87890335..87892797-chr4:87926492..87928312,3	MCF-7	breast:
3	chr4:87853531..87856106-chr4:87889167..87893034,3	K562	blood:
4	chr4:87885386..87887913-chr4:87890283..87891945,2	MCF-7	breast:
5	chr4:87891330..87894052-chr4:87927164..87929617,3	K562	blood:

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10032244	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10050311	0.87[CEU][hapmap]
rs1010902	0.85[EUR][1000 genomes]
rs1010903	0.86[EUR][1000 genomes]
rs10516786	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11729622	0.85[ASN][1000 genomes]
rs13126334	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs13127250	0.85[ASN][1000 genomes]
rs1447994	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17012170	0.93[CEU][hapmap];0.95[EUR][1000 genomes]
rs17012200	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17012213	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17012216	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17694112	0.81[CEU][hapmap]
rs17751427	0.92[EUR][1000 genomes]
rs17751557	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs17752307	0.84[EUR][1000 genomes]
rs1985944	0.86[EUR][1000 genomes]
rs2053769	0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2053770	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2053771	0.95[EUR][1000 genomes]
rs2287147	0.81[CEU][hapmap]
rs340626	0.81[ASN][1000 genomes]
rs340630	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs340633	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs340636	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs340637	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs340638	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs340639	0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs340641	0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs340642	0.92[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs340643	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs340648	0.84[ASN][1000 genomes]
rs340650	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs340651	0.81[ASN][1000 genomes]
rs375795	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs388401	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4693153	0.93[EUR][1000 genomes]
rs4693154	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs4693795	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs4693796	0.92[ASN][1000 genomes]
rs4693798	0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs4693800	0.85[ASN][1000 genomes]
rs55698195	0.84[EUR][1000 genomes]
rs55831707	0.93[EUR][1000 genomes]
rs55851914	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55913164	0.84[EUR][1000 genomes]
rs56201068	0.84[EUR][1000 genomes]
rs58633957	0.81[ASN][1000 genomes]
rs58822039	0.80[ASN][1000 genomes]
rs61651372	0.93[EUR][1000 genomes]
rs6531941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6531948	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6811587	0.86[ASN][1000 genomes]
rs6839933	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs72667703	0.86[EUR][1000 genomes]
rs72667705	0.85[EUR][1000 genomes]
rs72667716	0.93[EUR][1000 genomes]
rs72667721	0.93[EUR][1000 genomes]
rs72667724	0.93[EUR][1000 genomes]
rs72667727	0.94[EUR][1000 genomes]
rs72667735	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72667736	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72667737	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72667739	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72667741	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7657530	0.91[CHB][hapmap]
rs7665282	0.84[EUR][1000 genomes]
rs867196	0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9715807	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87868400-87891800	Weak transcription	Esophagus	oesophagus
2	chr4:87868600-87898000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:87869800-87894000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr4:87872600-87926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:87878800-87891600	Weak transcription	NHEK	skin
6	chr4:87881000-87891800	Weak transcription	Lung	lung
7	chr4:87881000-87897600	Weak transcription	Brain Angular Gyrus	brain
8	chr4:87882000-87895400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr4:87882200-87895600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:87882400-87893800	Weak transcription	Colonic Mucosa	Colon
11	chr4:87882400-87898600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:87882600-87920200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:87882800-87891600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr4:87882800-87912400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:87883000-87891800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr4:87883800-87891800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:87883800-87891800	Weak transcription	Fetal Intestine Large	intestine
18	chr4:87883800-87894200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr4:87884200-87893800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr4:87884200-87894000	Weak transcription	Fetal Intestine Small	intestine
21	chr4:87885000-87891800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:87885000-87894200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:87885000-87894200	Weak transcription	HMEC	breast
24	chr4:87886600-87898600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr4:87886800-87891800	Weak transcription	Fetal Heart	heart
26	chr4:87886800-87894200	Weak transcription	Hela-S3	cervix
27	chr4:87887000-87891800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:87887000-87892600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr4:87887400-87891600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr4:87887400-87891800	Weak transcription	Brain Hippocampus Middle	brain
31	chr4:87887400-87891800	Weak transcription	Colon Smooth Muscle	Colon
32	chr4:87887800-87891800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:87888000-87893400	Enhancers	HUVEC	blood vessel
34	chr4:87888200-87891600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:87888200-87895800	Weak transcription	Primary T cells from cord blood	blood
36	chr4:87888400-87891800	Weak transcription	Right Atrium	heart
37	chr4:87888400-87895000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr4:87888600-87892400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr4:87888600-87893400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:87888600-87893400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr4:87888800-87891800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:87888800-87891800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr4:87888800-87898800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr4:87889200-87891800	Weak transcription	Spleen	Spleen
45	chr4:87889200-87894000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr4:87889200-87894200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr4:87889200-87895400	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr4:87889400-87894200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr4:87889800-87891600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr4:87889800-87891600	Weak transcription	Rectal Smooth Muscle	rectum

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