Variant report

Variant	rs2967429
Chromosome Location	chr19:37096566-37096567
allele	A/C/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	chr19:37095596-37096798	GM15510	blood:	n/a	n/a
2	PAX5	chr19:37096281-37096886	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:37095588-37096843	GM19099	blood:	n/a	n/a
4	POLR2A	chr19:37095662-37096632	GM12891	blood:	n/a	n/a
5	POLR2A	chr19:37095559-37096914	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:37095602-37096934	GM12878	blood:	n/a	n/a
7	MAX	chr19:37095553-37097056	GM12878	blood:	n/a	chr19:37095706-37095716 chr19:37096192-37096201
8	YY1	chr19:37096272-37096713	GM12892	blood:	n/a	n/a
9	BACH1	chr19:37095537-37096710	H1-hESC	embryonic stem cell:	n/a	n/a
10	KAP1	chr19:37096414-37096952	HEK293	kidney:	n/a	n/a
11	POLR2A	chr19:37095691-37096592	HepG2	liver:	n/a	n/a
12	CHD2	chr19:37095541-37097003	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:37095803-37096791	PFSK-1	brain:	n/a	n/a
14	YY1	chr19:37096423-37096683	GM12891	blood:	n/a	n/a
15	POLR2A	chr19:37095423-37097058	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:37095539-37096687	HepG2	liver:	n/a	n/a
17	SIN3A	chr19:37095616-37096913	H1-hESC	embryonic stem cell:	n/a	n/a
18	MEF2C	chr19:37096462-37096858	GM12878	blood:	n/a	chr19:37096719-37096733 chr19:37096717-37096738 chr19:37096720-37096731 chr19:37096717-37096738 chr19:37096721-37096732 chr19:37096719-37096734 chr19:37096722-37096731 chr19:37096718-37096734 chr19:37096717-37096738
19	POLR2A	chr19:37095624-37096704	GM12892	blood:	n/a	n/a
20	TCF12	chr19:37095414-37096700	ECC-1	luminal epithelium:	n/a	n/a
21	HEY1	chr19:37095993-37096638	HepG2	liver:	n/a	chr19:37096198-37096213
22	TBP	chr19:37096028-37097015	GM12878	blood:	n/a	n/a
23	MAX	chr19:37095431-37097005	HepG2	liver:	n/a	chr19:37095706-37095716 chr19:37096192-37096201
24	BHLHE40	chr19:37095571-37097079	GM12878	blood:	n/a	n/a
25	TBP	chr19:37096517-37096591	HepG2	liver:	n/a	n/a
26	POLR2A	chr19:37095459-37097023	H1-neurons	neurons:	n/a	n/a
27	POLR2A	chr19:37095760-37096620	GM12892	blood:	n/a	n/a
28	POLR2A	chr19:37095462-37096908	GM12878	blood:	n/a	n/a
29	MAX	chr19:37095414-37096988	ECC-1	luminal epithelium:	n/a	chr19:37095706-37095716 chr19:37096192-37096201
30	POLR2A	chr19:37095580-37096858	GM18505	blood:	n/a	n/a
31	POLR2A	chr19:37095498-37097017	HL-60	blood:	n/a	n/a
32	MXI1	chr19:37095362-37096612	HepG2	liver:	n/a	n/a
33	RELA	chr19:37095662-37096920	GM19099	blood:	n/a	n/a
34	MEF2C	chr19:37096356-37097000	GM12878	blood:	n/a	chr19:37096719-37096733 chr19:37096717-37096738 chr19:37096720-37096731 chr19:37096717-37096738 chr19:37096721-37096732 chr19:37096719-37096734 chr19:37096722-37096731 chr19:37096718-37096734 chr19:37096717-37096738
35	ZBTB7A	chr19:37095557-37096703	ECC-1	luminal epithelium:	n/a	n/a
36	POLR2A	chr19:37095587-37096717	GM18951	blood:	n/a	n/a
37	YY1	chr19:37096300-37096736	GM12878	blood:	n/a	n/a
38	POLR2A	chr19:37095831-37096710	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr19:37095821-37096658	GM12878	blood:	n/a	n/a
40	CTBP2	chr19:37095624-37096767	H1-hESC	embryonic stem cell:	n/a	n/a
41	ELF1	chr19:37095918-37096683	GM12878	blood:	n/a	n/a
42	HEY1	chr19:37095673-37096726	HepG2	liver:	n/a	chr19:37096198-37096213
43	POLR2A	chr19:37095389-37096812	SK-N-MC	brain:	n/a	n/a
44	POLR2A	chr19:37095870-37096592	HUVEC	blood vessel:	n/a	n/a
45	MXI1	chr19:37096515-37097007	GM12878	blood:	n/a	n/a
46	MAX	chr19:37095560-37096857	NB4	blood:	n/a	chr19:37095706-37095716 chr19:37096192-37096201
47	POLR2A	chr19:37095867-37096655	H1-hESC	embryonic stem cell:	n/a	n/a
48	HMGN3	chr19:37096393-37096625	K562	blood:	n/a	n/a
49	MAZ	chr19:37095365-37096628	GM12878	blood:	n/a	chr19:37095706-37095716 chr19:37096192-37096201
50	TAF1	chr19:37096053-37096713	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37094753..37097505-chr19:37099237..37101505,2	K562	blood:

Variant related genes	Relation type
ZNF529	TF binding region
ZNF382	TF binding region
ENSG00000161298	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1035777	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs10402182	0.95[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs10403456	0.84[ASN][1000 genomes]
rs10407919	0.90[ASN][1000 genomes]
rs11084861	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11666769	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11667894	0.90[ASN][1000 genomes]
rs11668432	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11668689	0.94[ASN][1000 genomes]
rs11669816	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11670914	0.83[ASN][1000 genomes]
rs11671382	0.86[ASN][1000 genomes]
rs11672098	0.82[ASN][1000 genomes]
rs12608459	0.93[ASN][1000 genomes]
rs12608512	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12610555	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12610572	0.83[ASN][1000 genomes]
rs1357879	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap]
rs1464830	0.92[ASN][1000 genomes]
rs1464831	0.92[ASN][1000 genomes]
rs1525133	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs1673082	0.86[ASN][1000 genomes]
rs17272386	1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1985980	0.92[ASN][1000 genomes]
rs2052728	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2162296	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2194976	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2912399	0.92[ASN][1000 genomes]
rs2912400	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2912404	0.89[ASN][1000 genomes]
rs2912408	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2912412	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2912440	0.89[ASN][1000 genomes]
rs2912442	0.90[ASN][1000 genomes]
rs2912443	0.90[ASN][1000 genomes]
rs2912444	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2912446	1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2945964	0.90[ASN][1000 genomes]
rs2945978	0.85[ASN][1000 genomes]
rs2967427	0.94[ASN][1000 genomes]
rs2967436	0.95[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2967437	0.92[ASN][1000 genomes]
rs2967438	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2967439	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2967440	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2967442	1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2967459	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs2967461	0.87[ASN][1000 genomes]
rs2967463	0.94[ASN][1000 genomes]
rs2967464	0.90[ASN][1000 genomes]
rs2967473	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs2967545	0.80[ASN][1000 genomes]
rs3096620	1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs3096637	0.90[ASN][1000 genomes]
rs3108593	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3108605	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs35299345	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4806338	0.84[ASN][1000 genomes]
rs4806339	0.90[ASN][1000 genomes]
rs4806349	0.83[ASN][1000 genomes]
rs55940011	0.82[ASN][1000 genomes]
rs60213885	0.83[ASN][1000 genomes]
rs60297398	0.90[ASN][1000 genomes]
rs61457535	0.90[ASN][1000 genomes]
rs61628442	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6510551	0.92[ASN][1000 genomes]
rs66717711	0.83[ASN][1000 genomes]
rs66783290	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67258954	0.84[ASN][1000 genomes]
rs67995015	0.90[ASN][1000 genomes]
rs68012004	0.90[ASN][1000 genomes]
rs7246216	0.84[ASN][1000 genomes]
rs7251805	0.94[ASN][1000 genomes]
rs73609113	0.83[ASN][1000 genomes]
rs7507224	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8100381	1.00[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs8108985	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs826987	0.82[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	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
7	esv3434386	chr19:37073454-37114509	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37094000-37097200	ZNF genes & repeats	Liver	Liver
2	chr19:37095000-37096600	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr19:37095000-37096600	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr19:37095000-37096600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
5	chr19:37095000-37096800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:37095000-37097200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:37095000-37097200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
8	chr19:37095200-37096600	Active TSS	Left Ventricle	heart
9	chr19:37095200-37096600	Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr19:37095200-37096600	Active TSS	NHLF	lung
11	chr19:37095200-37096800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
12	chr19:37095200-37096800	Active TSS	Colon Smooth Muscle	Colon
13	chr19:37095200-37096800	Active TSS	Fetal Intestine Small	intestine
14	chr19:37095200-37096800	Active TSS	Fetal Kidney	kidney
15	chr19:37095200-37096800	Active TSS	Psoas Muscle	Psoas
16	chr19:37095200-37096800	Active TSS	Rectal Smooth Muscle	rectum
17	chr19:37095200-37096800	Active TSS	HSMM	muscle
18	chr19:37095200-37097000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:37095200-37097000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:37095200-37097000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr19:37095200-37097000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:37095200-37097000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr19:37095200-37097000	Active TSS	Colonic Mucosa	Colon
24	chr19:37095200-37097000	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr19:37095200-37097000	Active TSS	Fetal Muscle Trunk	muscle
26	chr19:37095200-37097000	ZNF genes & repeats	Gastric	stomach
27	chr19:37095200-37097000	Active TSS	Right Atrium	heart
28	chr19:37095200-37097200	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr19:37095200-37097200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
30	chr19:37095200-37097200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
31	chr19:37095200-37097200	Active TSS	NHDF-Ad	bronchial
32	chr19:37095200-37097400	ZNF genes & repeats	Lung	lung
33	chr19:37095400-37096600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr19:37095400-37096600	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr19:37095400-37096600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr19:37095400-37096600	Active TSS	Fetal Heart	heart
37	chr19:37095400-37096600	Active TSS	GM12878-XiMat	blood
38	chr19:37095400-37096800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:37095400-37096800	Active TSS	H9 Cell Line	embryonic stem cell
40	chr19:37095400-37096800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr19:37095400-37096800	Active TSS	Muscle Satellite Cultured Cells	--
42	chr19:37095400-37096800	Active TSS	Brain Cingulate Gyrus	brain
43	chr19:37095400-37096800	Active TSS	Ovary	ovary
44	chr19:37095400-37096800	Active TSS	Small Intestine	intestine
45	chr19:37095400-37097000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
46	chr19:37095400-37097000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr19:37095400-37097000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr19:37095400-37097000	Active TSS	HMEC	breast
49	chr19:37095400-37097200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
50	chr19:37095400-37097200	Active TSS	Rectal Mucosa Donor 31	rectum

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