Variant report

Variant	rs3729709
Chromosome Location	chr19:55667806-55667807
allele	A/G
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	ELF1	chr19:55667602-55667973	GM12878	blood:	n/a	n/a
2	ETS1	chr19:55667776-55667963	K562	blood:	n/a	chr19:55667878-55667887 chr19:55667876-55667886 chr19:55667876-55667887 chr19:55667920-55667931
3	STAT3	chr19:55667806-55668053	MCF10A-Er-Src	breast:	n/a	n/a
4	EGR1	chr19:55667590-55668125	H1-hESC	embryonic stem cell:	n/a	chr19:55667872-55667885 chr19:55667878-55667887 chr19:55667869-55667883 chr19:55667918-55667932
5	SPI1	chr19:55667770-55667964	K562	blood:	n/a	n/a
6	TCF12	chr19:55667758-55668289	A549	lung:	n/a	n/a
7	SIN3A	chr19:55667439-55668479	H1-hESC	embryonic stem cell:	n/a	n/a
8	GABPA	chr19:55667681-55668036	K562	blood:	n/a	chr19:55667871-55667880
9	EGR1	chr19:55667606-55668116	K562	blood:	n/a	chr19:55667872-55667885 chr19:55667878-55667887 chr19:55667869-55667883 chr19:55667918-55667932
10	POLR2A	chr19:55667406-55669499	K562	blood:	n/a	n/a
11	SP4	chr19:55667707-55668300	H1-hESC	embryonic stem cell:	n/a	chr19:55667918-55667934 chr19:55667916-55667932 chr19:55667918-55667929 chr19:55667899-55667915 chr19:55668151-55668167 chr19:55667901-55667912 chr19:55667847-55667863 chr19:55667869-55667885 chr19:55667867-55667883
12	POLR2A	chr19:55667546-55668102	HCT-116	colon:	n/a	n/a
13	POLR2A	chr19:55667659-55667937	HepG2	liver:	n/a	n/a
14	SP4	chr19:55667620-55668443	H1-hESC	embryonic stem cell:	n/a	chr19:55667918-55667934 chr19:55667916-55667932 chr19:55667918-55667929 chr19:55667899-55667915 chr19:55668151-55668167 chr19:55667901-55667912 chr19:55668319-55668335 chr19:55667847-55667863 chr19:55667869-55667885 chr19:55667867-55667883 chr19:55668321-55668337
15	POLR2A	chr19:55667638-55667883	HepG2	liver:	n/a	n/a
16	MAX	chr19:55667783-55668073	K562	blood:	n/a	n/a
17	POLR2A	chr19:55667593-55667976	K562	blood:	n/a	n/a
18	SP1	chr19:55667587-55668401	A549	lung:	n/a	chr19:55667850-55667860 chr19:55667918-55667930 chr19:55668322-55668331 chr19:55668344-55668356 chr19:55667869-55667881 chr19:55668153-55668165 chr19:55667919-55667933 chr19:55668321-55668333 chr19:55667870-55667880 chr19:55668322-55668331 chr19:55668154-55668164 chr19:55668344-55668356 chr19:55667918-55667929 chr19:55667920-55667929 chr19:55667870-55667880 chr19:55667919-55667928 chr19:55668153-55668165 chr19:55667869-55667881 chr19:55667870-55667879 chr19:55667901-55667912 chr19:55667870-55667879 chr19:55667918-55667930 chr19:55668321-55668333 chr19:55668323-55668332 chr19:55667871-55667880 chr19:55668154-55668164 chr19:55667870-55667884 chr19:55668322-55668336
19	SPI1	chr19:55667781-55667995	K562	blood:	n/a	n/a
20	MAX	chr19:55667660-55668270	ECC-1	luminal epithelium:	n/a	chr19:55668118-55668127
21	E2F6	chr19:55667675-55668381	H1-hESC	embryonic stem cell:	n/a	chr19:55668323-55668332
22	TBP	chr19:55667648-55667833	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr19:55667683-55667860	A549	lung:	n/a	n/a
24	POLR2A	chr19:55667569-55667993	K562	blood:	n/a	n/a
25	ELK1	chr19:55667562-55668111	K562	blood:	n/a	n/a
26	ELF1	chr19:55667568-55668024	K562	blood:	n/a	n/a
27	HEY1	chr19:55667633-55667935	K562	blood:	n/a	n/a
28	GABPA	chr19:55667465-55668164	K562	blood:	n/a	chr19:55667871-55667880
29	TBP	chr19:55667647-55668141	K562	blood:	n/a	n/a
30	MAX	chr19:55667679-55668262	ECC-1	luminal epithelium:	n/a	chr19:55668118-55668127
31	TAF1	chr19:55667712-55667941	K562	blood:	n/a	n/a
32	NR2F2	chr19:55667449-55668379	K562	blood:	n/a	n/a
33	ELF1	chr19:55667718-55667979	HepG2	liver:	n/a	n/a
34	POLR2A	chr19:55667701-55667823	HepG2	liver:	n/a	n/a
35	E2F6	chr19:55667725-55668307	H1-hESC	embryonic stem cell:	n/a	n/a
36	EGR1	chr19:55667557-55668318	HCT-116	colon:	n/a	chr19:55667872-55667885 chr19:55667878-55667887 chr19:55667869-55667883 chr19:55667918-55667932
37	SP1	chr19:55667311-55668566	H1-hESC	embryonic stem cell:	n/a	chr19:55667850-55667860 chr19:55667918-55667930 chr19:55668322-55668331 chr19:55668344-55668356 chr19:55667869-55667881 chr19:55668153-55668165 chr19:55667919-55667933 chr19:55668321-55668333 chr19:55667870-55667880 chr19:55668322-55668331 chr19:55668154-55668164 chr19:55668344-55668356 chr19:55667918-55667929 chr19:55667920-55667929 chr19:55667870-55667880 chr19:55667919-55667928 chr19:55668153-55668165 chr19:55667869-55667881 chr19:55667870-55667879 chr19:55667901-55667912 chr19:55667870-55667879 chr19:55667918-55667930 chr19:55668321-55668333 chr19:55668323-55668332 chr19:55667871-55667880 chr19:55668154-55668164 chr19:55667870-55667884 chr19:55668322-55668336
38	ZBTB7A	chr19:55667523-55667996	K562	blood:	n/a	n/a
39	RCOR1	chr19:55667698-55668250	K562	blood:	n/a	n/a
40	POLR2A	chr19:55667601-55668086	HCT-116	colon:	n/a	n/a
41	TAF1	chr19:55667563-55667894	H1-hESC	embryonic stem cell:	n/a	n/a
42	RCOR1	chr19:55667761-55668371	K562	blood:	n/a	n/a
43	IRF1	chr19:55667643-55668435	K562	blood:	n/a	chr19:55668319-55668333 chr19:55668151-55668165 chr19:55667916-55667930 chr19:55667867-55667881
44	TBL1XR1	chr19:55667650-55667850	K562	blood:	n/a	n/a
45	ELF1	chr19:55667636-55668411	K562	blood:	n/a	n/a
46	CCNT2	chr19:55667549-55668057	K562	blood:	n/a	n/a
47	MAX	chr19:55667282-55668377	K562	blood:	n/a	chr19:55668118-55668127
48	HMGN3	chr19:55667447-55668140	K562	blood:	n/a	n/a
49	SP1	chr19:55667583-55668352	K562	blood:	n/a	chr19:55667850-55667860 chr19:55667918-55667930 chr19:55668322-55668331 chr19:55667869-55667881 chr19:55668153-55668165 chr19:55667919-55667933 chr19:55668321-55668333 chr19:55667870-55667880 chr19:55668322-55668331 chr19:55668154-55668164 chr19:55667918-55667929 chr19:55667920-55667929 chr19:55667870-55667880 chr19:55667919-55667928 chr19:55668153-55668165 chr19:55667869-55667881 chr19:55667870-55667879 chr19:55667901-55667912 chr19:55667870-55667879 chr19:55667918-55667930 chr19:55668321-55668333 chr19:55668323-55668332 chr19:55667871-55667880 chr19:55668154-55668164 chr19:55667870-55667884 chr19:55668322-55668336
50	SP1	chr19:55667520-55668372	H1-hESC	embryonic stem cell:	n/a	chr19:55667850-55667860 chr19:55667918-55667930 chr19:55668322-55668331 chr19:55668344-55668356 chr19:55667869-55667881 chr19:55668153-55668165 chr19:55667919-55667933 chr19:55668321-55668333 chr19:55667870-55667880 chr19:55668322-55668331 chr19:55668154-55668164 chr19:55668344-55668356 chr19:55667918-55667929 chr19:55667920-55667929 chr19:55667870-55667880 chr19:55667919-55667928 chr19:55668153-55668165 chr19:55667869-55667881 chr19:55667870-55667879 chr19:55667901-55667912 chr19:55667870-55667879 chr19:55667918-55667930 chr19:55668321-55668333 chr19:55668323-55668332 chr19:55667871-55667880 chr19:55668154-55668164 chr19:55667870-55667884 chr19:55668322-55668336

No.	Distal block	Cell Line	Cell type
1	chr19:55667256..55669360-chr19:55970897..55972567,2	K562	blood:
2	chr19:55666494..55670422-chr19:55672733..55675574,3	K562	blood:
3	chr19:55658387..55665037-chr19:55666866..55670836,8	K562	blood:
4	chr19:55627863..55630542-chr19:55666165..55668037,2	K562	blood:
5	chr19:55666595..55669878-chr19:55917801..55921094,4	K562	blood:
6	chr19:55627602..55630542-chr19:55666165..55668443,2	K562	blood:
7	chr19:55655324..55657835-chr19:55666870..55669444,2	K562	blood:
8	chr19:55666873..55668722-chr19:55676430..55678695,2	K562	blood:
9	chr19:55627370..55629030-chr19:55666382..55669249,2	MCF-7	breast:

Variant related genes	Relation type
TNNI3	TF binding region
ENSG00000267577	TF binding region
ENSG00000125503	Chromatin interaction
ENSG00000239137	Chromatin interaction
ENSG00000105048	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000167646	Chromatin interaction
ENSG00000063241	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10416615	1.00[ASW][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs2365725	1.00[JPT][hapmap]
rs3729708	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3848617	1.00[JPT][hapmap]
rs6509931	0.81[TSI][hapmap]
rs6509932	0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534462	chr19:55028722-55683018	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv912451	chr19:55595687-55680746	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55666400-55669400	Active TSS	Left Ventricle	heart
2	chr19:55667200-55668000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:55667200-55668400	Active TSS	H1 Cell Line	embryonic stem cell
4	chr19:55667200-55668400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr19:55667200-55668400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:55667200-55668600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
7	chr19:55667200-55668600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
8	chr19:55667200-55668800	Active TSS	H9 Cell Line	embryonic stem cell
9	chr19:55667200-55669200	Active TSS	Right Atrium	heart
10	chr19:55667400-55668000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr19:55667400-55668200	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr19:55667400-55668200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr19:55667400-55668200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
14	chr19:55667400-55668200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:55667400-55668200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:55667400-55668200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr19:55667400-55668200	Bivalent Enhancer	Brain Substantia Nigra	brain
18	chr19:55667400-55668200	Bivalent Enhancer	Fetal Lung	lung
19	chr19:55667400-55668200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
20	chr19:55667400-55668400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
21	chr19:55667400-55668400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
22	chr19:55667400-55668400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr19:55667400-55668400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
24	chr19:55667400-55668400	Active TSS	A549	lung
25	chr19:55667400-55668600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr19:55667400-55668600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
27	chr19:55667400-55668600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr19:55667400-55668600	Enhancers	Gastric	stomach
29	chr19:55667400-55668600	Enhancers	Pancreas	Pancrea
30	chr19:55667400-55668800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr19:55667400-55668800	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr19:55667400-55668800	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr19:55667400-55668800	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr19:55667400-55668800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr19:55667400-55668800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
36	chr19:55667400-55668800	Bivalent/Poised TSS	HepG2	liver
37	chr19:55667400-55669000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
38	chr19:55667400-55669000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr19:55667400-55669000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
40	chr19:55667400-55669000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
41	chr19:55667400-55669000	ZNF genes & repeats	Spleen	Spleen
42	chr19:55667400-55669200	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr19:55667400-55669400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
44	chr19:55667400-55670000	Bivalent Enhancer	Placenta	Placenta
45	chr19:55667600-55668000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:55667600-55668000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
47	chr19:55667600-55668000	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
48	chr19:55667600-55668000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
49	chr19:55667600-55668000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
50	chr19:55667600-55668000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain

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