Variant report

Variant	rs11071400
Chromosome Location	chr15:59183646-59183647
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:59183176-59184509	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59182773..59184278-chr15:59224133..59226486,2	MCF-7	breast:

Variant related genes	Relation type
SLTM	TF binding region
ENSG00000137776	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10162821	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518991	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10518992	0.82[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1078001	0.92[ASN][1000 genomes]
rs11071401	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11630160	0.82[CEU][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11630265	0.83[AFR][1000 genomes]
rs11636723	0.82[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11637077	0.82[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11856640	0.82[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs11858989	0.82[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12148858	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12443436	0.80[ASN][1000 genomes]
rs12595482	0.86[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12708456	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12901551	0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs12909894	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12914723	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12916751	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17302038	0.93[ASN][1000 genomes]
rs17302045	0.82[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs173214	0.82[CEU][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2013117	0.86[ASN][1000 genomes]
rs2270664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279719	0.84[ASN][1000 genomes]
rs28473013	0.94[ASN][1000 genomes]
rs28529423	0.94[ASN][1000 genomes]
rs28538484	0.95[ASN][1000 genomes]
rs28641638	0.82[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs28709922	0.94[ASN][1000 genomes]
rs3145	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.99[MKK][hapmap];0.94[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35477914	0.95[ASN][1000 genomes]
rs431414	0.80[CEU][hapmap]
rs4774315	0.83[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775101	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67851431	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71407077	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7173317	0.94[ASN][1000 genomes]
rs793571	0.86[EUR][1000 genomes]
rs8035628	0.91[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[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	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers 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	87 gene(s)	inside rSNPs	diseases
2	esv1826703	chr15:59005922-59213678	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1798487	chr15:59027139-59213678	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv1035640	chr15:59105360-59190930	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv904270	chr15:59140329-59238415	Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	esv1850946	chr15:59174539-59429160	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59167000-59193200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr15:59167800-59187600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr15:59167800-59194000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:59168000-59188800	Strong transcription	Fetal Muscle Leg	muscle
5	chr15:59168200-59189000	Strong transcription	Fetal Muscle Trunk	muscle
6	chr15:59168200-59202200	Strong transcription	Fetal Thymus	thymus
7	chr15:59168400-59188400	Strong transcription	Stomach Smooth Muscle	stomach
8	chr15:59168400-59188800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:59168400-59193200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr15:59168400-59193200	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:59168400-59206600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr15:59168400-59209600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr15:59168600-59188600	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chr15:59168600-59189400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:59168600-59193000	Strong transcription	A549	lung
16	chr15:59168600-59195800	Strong transcription	Dnd41	blood
17	chr15:59168600-59202400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr15:59168600-59209800	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr15:59168600-59220000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr15:59168800-59190200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:59168800-59193200	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr15:59168800-59193200	Strong transcription	Adipose Nuclei	Adipose
23	chr15:59169000-59190400	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:59169000-59193000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr15:59169000-59193200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr15:59169000-59193400	Strong transcription	K562	blood
27	chr15:59169000-59209800	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr15:59169000-59210600	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr15:59169200-59193200	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr15:59169200-59193800	Strong transcription	NHDF-Ad	bronchial
31	chr15:59169200-59195000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr15:59169200-59223200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:59169400-59187000	Strong transcription	Brain Germinal Matrix	brain
34	chr15:59169400-59188800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr15:59169400-59188800	Strong transcription	HepG2	liver
36	chr15:59169400-59189600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr15:59169400-59193000	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr15:59169400-59193400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr15:59169400-59193800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:59169400-59210000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr15:59169400-59211800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr15:59169600-59193600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr15:59170000-59189400	Strong transcription	Fetal Intestine Large	intestine
44	chr15:59170000-59190200	Strong transcription	Rectal Smooth Muscle	rectum
45	chr15:59170000-59193400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr15:59170000-59194000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr15:59170000-59194000	Strong transcription	Liver	Liver
48	chr15:59170000-59209400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr15:59170200-59185000	Strong transcription	Brain Hippocampus Middle	brain
50	chr15:59170200-59185000	Strong transcription	Left Ventricle	heart

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