Variant report

Variant	rs2139647
Chromosome Location	chr15:45996897-45996898
allele	G/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	chr15:45996635-45997010	H1-hESC	embryonic stem cell:	n/a	n/a
2	TEAD4	chr15:45996679-45997065	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr15:45996380-45997154	H1-hESC	embryonic stem cell:	n/a	n/a
4	SIN3A	chr15:45996123-45997193	H1-hESC	embryonic stem cell:	n/a	chr15:45996441-45996450
5	POLR2A	chr15:45996735-45996932	HUVEC	blood vessel:	n/a	n/a
6	TEAD4	chr15:45996754-45996978	H1-hESC	embryonic stem cell:	n/a	n/a
7	TCF7L2	chr15:45996503-45997038	PANC-1	pancreas:	n/a	n/a
8	ZNF143	chr15:45996082-45997025	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr15:45996515-45997189	PANC-1	pancreas:	n/a	n/a
10	GTF2F1	chr15:45996784-45996989	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr15:45996489-45997118	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr15:45996546-45997183	PANC-1	pancreas:	n/a	n/a
13	MAX	chr15:45995911-45997033	H1-hESC	embryonic stem cell:	n/a	n/a
14	E2F6	chr15:45995821-45997041	H1-hESC	embryonic stem cell:	n/a	chr15:45996532-45996540 chr15:45996529-45996541 chr15:45996533-45996540 chr15:45996525-45996539 chr15:45996532-45996540 chr15:45996533-45996540 chr15:45996533-45996540 chr15:45996530-45996545 chr15:45996531-45996541
15	POLR2A	chr15:45996462-45997088	U87	brain:	n/a	n/a
16	CTCF	chr15:45996800-45996950	HPAF	blood vessel:	n/a	n/a
17	CTCF	chr15:45996760-45996910	GM12865	blood:	n/a	n/a
18	POLR2A	chr15:45996745-45996981	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr15:45996616-45997045	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr15:45996675-45997078	H1-hESC	embryonic stem cell:	n/a	n/a
21	TAF1	chr15:45996496-45997160	H1-hESC	embryonic stem cell:	n/a	n/a
22	ELF1	chr15:45996442-45996946	GM12878	blood:	n/a	n/a
23	JUND	chr15:45996766-45997089	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAX	chr15:45995811-45997022	H1-hESC	embryonic stem cell:	n/a	n/a
25	TAF1	chr15:45996641-45997064	H1-hESC	embryonic stem cell:	n/a	n/a
26	CHD1	chr15:45996712-45996998	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr15:45996620-45997148	U87	brain:	n/a	n/a
28	CHD2	chr15:45996160-45997083	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr15:45996800-45996950	HCPEpiC	choroid plexus:	n/a	n/a
30	TBP	chr15:45996613-45997001	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAX	chr15:45995903-45996944	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTBP2	chr15:45996170-45997065	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr15:45996780-45996930	HCPEpiC	choroid plexus:	n/a	n/a
34	MYC	chr15:45996743-45996903	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr15:45996620-45997109	U87	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000259200	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10643	1.00[ASN][1000 genomes]
rs11629585	1.00[ASN][1000 genomes]
rs11634640	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2413787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56108595	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62006179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62008310	1.00[ASN][1000 genomes]
rs62008318	1.00[ASN][1000 genomes]
rs62008319	1.00[ASN][1000 genomes]
rs62008320	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62008321	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72715101	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904189	chr15:45821158-46298458	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv904191	chr15:45902779-46381874	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv523136	chr15:45990780-46158407	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45996000-45997800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr15:45996000-45998000	Active TSS	H9 Cell Line	embryonic stem cell
3	chr15:45996000-45998000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:45996000-45998200	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr15:45996200-45997200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:45996200-45997200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr15:45996200-45997800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:45996200-45998200	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr15:45996200-45998200	Active TSS	H1 Cell Line	embryonic stem cell
10	chr15:45996200-45998200	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr15:45996200-45998200	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr15:45996400-45997000	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr15:45996400-45997000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
14	chr15:45996400-45997000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
15	chr15:45996400-45997000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr15:45996400-45997000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr15:45996400-45997000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr15:45996400-45997000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr15:45996400-45997000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
20	chr15:45996400-45997000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
21	chr15:45996400-45997000	Flanking Active TSS	Ovary	ovary
22	chr15:45996400-45997000	Flanking Active TSS	Right Ventricle	heart
23	chr15:45996400-45997000	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
24	chr15:45996400-45997000	Enhancers	Spleen	Spleen
25	chr15:45996400-45997200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
26	chr15:45996400-45997200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
27	chr15:45996400-45997200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:45996400-45997200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:45996400-45997200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
30	chr15:45996400-45997200	Bivalent/Poised TSS	Fetal Kidney	kidney
31	chr15:45996400-45997200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
32	chr15:45996400-45997200	Enhancers	Lung	lung
33	chr15:45996400-45997200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr15:45996400-45997600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr15:45996400-45997600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr15:45996400-45997600	Bivalent/Poised TSS	Fetal Brain Female	brain
37	chr15:45996400-45997600	Bivalent/Poised TSS	NH-A	brain
38	chr15:45996400-45997800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
39	chr15:45996400-45998000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr15:45996400-45998000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr15:45996400-45998000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:45996400-45998000	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr15:45996400-45998000	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr15:45996400-45998000	Active TSS	Brain Anterior Caudate	brain
45	chr15:45996400-45998000	Active TSS	Duodenum Mucosa	Duodenum
46	chr15:45996400-45998000	Active TSS	Rectal Smooth Muscle	rectum
47	chr15:45996400-45998200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:45996400-45998200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:45996400-45998200	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr15:45996400-45998200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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