Variant report

Variant	rs12976582
Chromosome Location	chr19:19779706-19779707
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	NFYA	chr19:19779283-19779846	GM12878	blood:	n/a	chr19:19779573-19779586 chr19:19779544-19779557
2	MAX	chr19:19779320-19779875	K562	blood:	n/a	n/a
3	TBL1XR1	chr19:19779309-19779805	K562	blood:	n/a	n/a
4	HCFC1	chr19:19779084-19780265	Hela-S3	cervix:	n/a	n/a
5	EGR1	chr19:19779533-19779772	GM12878	blood:	n/a	n/a
6	GABPA	chr19:19779352-19780014	SK-N-SH	brain:	n/a	chr19:19779994-19780003
7	REST	chr19:19779135-19780108	H1-neurons	neurons:	n/a	chr19:19779960-19779973 chr19:19779662-19779682 chr19:19779662-19779682
8	MTA3	chr19:19778977-19779890	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:19778811-19780284	GM12892	blood:	n/a	n/a
10	POLR2A	chr19:19779380-19779952	HUVEC	blood vessel:	n/a	n/a
11	IRF3	chr19:19779422-19779738	HepG2	liver:	n/a	chr19:19779525-19779539
12	ATF2	chr19:19779453-19779906	GM12878	blood:	n/a	n/a
13	TAF1	chr19:19779390-19779963	A549	lung:	n/a	n/a
14	JUND	chr19:19779527-19779804	A549	lung:	n/a	chr19:19779638-19779647 chr19:19779650-19779664 chr19:19779612-19779626
15	ELF1	chr19:19779380-19780009	K562	blood:	n/a	chr19:19779757-19779768 chr19:19779784-19779796 chr19:19779758-19779767
16	SIN3AK20	chr19:19779505-19779951	SK-N-SH	brain:	n/a	n/a
17	REST	chr19:19779482-19779809	HepG2	liver:	n/a	chr19:19779662-19779682 chr19:19779662-19779682
18	POLR2A	chr19:19779271-19779957	SK-N-SH	brain:	n/a	n/a
19	ETS1	chr19:19779571-19779994	GM12878	blood:	n/a	n/a
20	MAX	chr19:19779255-19779940	MCF-7	breast:	n/a	n/a
21	POLR2A	chr19:19779120-19780148	SK-N-MC	brain:	n/a	n/a
22	ELF1	chr19:19779303-19780621	MCF-7	breast:	n/a	chr19:19780388-19780401 chr19:19779757-19779768 chr19:19779784-19779796 chr19:19779758-19779767
23	CBX3	chr19:19779599-19779849	K562	blood:	n/a	n/a
24	TAF1	chr19:19778941-19780043	GM12878	blood:	n/a	n/a
25	POLR2A	chr19:19779531-19779859	A549	lung:	n/a	n/a
26	POLR2A	chr19:19778954-19780049	GM15510	blood:	n/a	n/a
27	PML	chr19:19779428-19779907	MCF-7	breast:	n/a	n/a
28	POLR2A	chr19:19779026-19779958	GM12878	blood:	n/a	n/a
29	SP1	chr19:19779261-19779940	A549	lung:	n/a	chr19:19779590-19779604 chr19:19779527-19779536 chr19:19779525-19779537 chr19:19779525-19779537 chr19:19779352-19779363
30	FOXM1	chr19:19778796-19780032	GM12878	blood:	n/a	n/a
31	HEY1	chr19:19779491-19780236	K562	blood:	n/a	chr19:19779996-19780011 chr19:19779991-19780006
32	NR2F2	chr19:19779065-19779992	MCF-7	breast:	n/a	n/a
33	ZBTB7A	chr19:19779287-19780352	ECC-1	luminal epithelium:	n/a	n/a
34	REST	chr19:19779479-19780034	HL-60	blood:	n/a	chr19:19779960-19779973 chr19:19779662-19779682 chr19:19779662-19779682
35	POLR2A	chr19:19779426-19779842	HUVEC	blood vessel:	n/a	n/a
36	FOS	chr19:19779388-19779768	K562	blood:	n/a	chr19:19779638-19779647 chr19:19779650-19779664 chr19:19779612-19779626
37	CCNT2	chr19:19779419-19779987	K562	blood:	n/a	n/a
38	RFX5	chr19:19779406-19779847	Hela-S3	cervix:	n/a	n/a
39	PAX5	chr19:19779468-19779951	GM12892	blood:	n/a	n/a
40	E2F4	chr19:19779275-19779843	GM12878	blood:	n/a	chr19:19779631-19779638 chr19:19779630-19779642 chr19:19779630-19779639 chr19:19779631-19779638 chr19:19779631-19779638
41	SP2	chr19:19779232-19779766	HepG2	liver:	n/a	chr19:19779589-19779604
42	POLR2A	chr19:19778737-19779872	HepG2	liver:	n/a	n/a
43	POLR2A	chr19:19779500-19779857	HepG2	liver:	n/a	n/a
44	TCF7L2	chr19:19779260-19779990	HCT-116	colon:	n/a	n/a
45	YY1	chr19:19779007-19780020	HepG2	liver:	n/a	chr19:19779634-19779645 chr19:19779998-19780009
46	MYBL2	chr19:19778830-19779862	HepG2	liver:	n/a	n/a
47	ZBTB7A	chr19:19779524-19780243	K562	blood:	n/a	n/a
48	HEY1	chr19:19778866-19779941	HepG2	liver:	n/a	n/a
49	ELK1	chr19:19779657-19779838	K562	blood:	n/a	n/a
50	MAX	chr19:19779254-19780330	A549	lung:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:19779697-19779747	MCF-7	breast:	n/a
2	chr19:19779697-19779747	T-47D	breast:	n/a
3	chr19:19779697-19779747	BJ	skin:	n/a
4	chr19:19779697-19779747	AG04449	skin:	fetal
5	chr19:19779697-19779747	HCF	heart:	n/a
6	chr19:19779697-19779747	AG09319	gingival:	n/a
7	chr19:19779697-19779747	GM12878	blood:	n/a
8	chr19:19779697-19779747	HIPEpiC	eye:	n/a
9	chr19:19779697-19779747	NHDF-neo	bronchial:	n/a
10	chr19:19779697-19779747	HUVEC	blood vessel:	n/a
11	chr19:19779697-19779747	AoSMC	blood vessel:	n/a
12	chr19:19779697-19779747	PrEC	prostate:	n/a
13	chr19:19779697-19779747	Hela-S3	cervix:	n/a
14	chr19:19779697-19779747	K562	blood:	n/a
15	chr19:19779697-19779747	SK-N-SH	brain:	n/a
16	chr19:19779697-19779747	GM06990	blood:	n/a
17	chr19:19779697-19779747	HRPEpiC	eye:	n/a
18	chr19:19779697-19779747	CMK	blood:	n/a
19	chr19:19779697-19779747	NT2-D1	testis:	n/a
20	chr19:19779697-19779747	AG09309	skin:	n/a
21	chr19:19779697-19779747	ovcar-3	ovarian:	n/a
22	chr19:19779697-19779747	HRE	kidney:	n/a
23	chr19:19779697-19779747	HCM	heart:	n/a
24	chr19:19779697-19779747	PANC-1	pancreas:	n/a
25	chr19:19779697-19779747	RPTEC	kidney:	n/a
26	chr19:19779697-19779747	NH-A	brain:	n/a
27	chr19:19779697-19779747	ProgFib	skin:	n/a
28	chr19:19779697-19779747	SKMC	muscle:	n/a
29	chr19:19779697-19779747	ECC-1	luminal epithelium:	n/a
30	chr19:19779697-19779747	HEK293	kidney:	embryo
31	chr19:19779697-19779747	HRCEpiC	kidney:	n/a
32	chr19:19779697-19779747	HL-60	blood:	n/a
33	chr19:19779697-19779747	HCT-116	colon:	n/a
34	chr19:19779697-19779747	IMR90	lung:	fetal
35	chr19:19779697-19779747	SK-N-MC	brain:	n/a
36	chr19:19779697-19779747	U87	brain:	n/a
37	chr19:19779697-19779747	AG04450	lung:	fetal
38	chr19:19779697-19779747	GM12892	blood:	n/a
39	chr19:19779697-19779747	Caco-2	colon:	n/a
40	chr19:19779697-19779747	HPAEpiC	pulmonary alveolar:	n/a
41	chr19:19779697-19779747	NB4	blood:	n/a
42	chr19:19779697-19779747	HMEC	breast:	n/a
43	chr19:19779697-19779747	GM19239	blood:	n/a
44	chr19:19779697-19779747	HAEpiC	amniotic membrane:	n/a
45	chr19:19779697-19779747	SK-N-SH_RA	brain:	n/a
46	chr19:19779697-19779747	A549	lung:	n/a
47	chr19:19779697-19779747	SAEC	small airway:	n/a
48	chr19:19779697-19779747	LNCaP	prostate:	n/a
49	chr19:19779697-19779747	GM12891	blood:	n/a
50	chr19:19779697-19779747	Jurkat	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19779650..19782100-chr19:19976513..19978467,2	MCF-7	breast:
2	chr19:19779580..19781317-chr19:19788331..19791225,2	MCF-7	breast:
3	chr19:19772164..19776257-chr19:19777737..19781997,10	MCF-7	breast:

Variant related genes	Relation type
ZNF101	TF binding region
ZNF101	CpG island
ENSG00000105726	Chromatin interaction
ENSG00000256771	Chromatin interaction
ENSG00000181896	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10402516	0.84[ASN][1000 genomes]
rs10405234	0.82[ASN][1000 genomes]
rs10423311	0.82[ASN][1000 genomes]
rs11667828	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11670710	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12974308	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12976826	0.81[EUR][1000 genomes]
rs12980482	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12982049	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12982500	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12983292	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1433079	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16994684	0.83[EUR][1000 genomes]
rs16996174	0.83[EUR][1000 genomes]
rs16996227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288865	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2288867	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2304129	0.81[EUR][1000 genomes]
rs28472726	0.80[ASN][1000 genomes]
rs28635562	0.82[ASN][1000 genomes]
rs34558847	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35035906	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35445661	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35449009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35792080	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35801717	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3752152	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3794996	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4808209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808974	0.81[EUR][1000 genomes]
rs4808976	0.82[ASN][1000 genomes]
rs4808979	0.87[ASN][1000 genomes]
rs4808981	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7247142	0.91[ASN][1000 genomes]
rs7249670	0.99[ASN][1000 genomes]
rs7251924	0.95[ASN][1000 genomes]
rs74181147	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74181148	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74181149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74181150	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74181151	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv911309	chr19:19727042-19784891	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv911310	chr19:19753882-19784891	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
5	esv3330851	chr19:19755507-19852881	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19778200-19780400	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr19:19778200-19781000	Active TSS	Primary T cells from cord blood	blood
3	chr19:19778800-19780400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
4	chr19:19778800-19780400	Active TSS	Rectal Smooth Muscle	rectum
5	chr19:19778800-19780600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr19:19778800-19780600	Active TSS	Primary T killer memory cells from peripheral blood	blood
7	chr19:19778800-19780600	Active TSS	Brain Hippocampus Middle	brain
8	chr19:19778800-19781400	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr19:19778800-19781600	Active TSS	H9 Cell Line	embryonic stem cell
10	chr19:19779000-19780200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:19779000-19780200	Active TSS	Spleen	Spleen
12	chr19:19779000-19780400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr19:19779000-19780400	Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr19:19779000-19780400	Active TSS	Muscle Satellite Cultured Cells	--
15	chr19:19779000-19780400	Active TSS	Lung	lung
16	chr19:19779000-19780400	Active TSS	HSMM	muscle
17	chr19:19779000-19780400	Active TSS	Osteobl	bone
18	chr19:19779000-19780600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:19779000-19780600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr19:19779000-19780600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr19:19779000-19780600	Active TSS	Fetal Kidney	kidney
22	chr19:19779000-19780600	Active TSS	Fetal Lung	lung
23	chr19:19779000-19780600	Active TSS	Right Atrium	heart
24	chr19:19779000-19780600	Active TSS	NHEK	skin
25	chr19:19779000-19780800	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr19:19779000-19780800	Active TSS	Rectal Mucosa Donor 31	rectum
27	chr19:19779000-19781000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:19779000-19781000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:19779000-19781000	Active TSS	Esophagus	oesophagus
30	chr19:19779000-19781000	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr19:19779000-19781200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr19:19779000-19781200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr19:19779000-19781400	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr19:19779200-19779800	Active TSS	HepG2	liver
35	chr19:19779200-19780200	Active TSS	Aorta	Aorta
36	chr19:19779200-19780200	Active TSS	Brain Substantia Nigra	brain
37	chr19:19779200-19780200	Active TSS	Fetal Stomach	stomach
38	chr19:19779200-19780200	Active TSS	Ovary	ovary
39	chr19:19779200-19780400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr19:19779200-19780400	Active TSS	Brain Angular Gyrus	brain
41	chr19:19779200-19780400	Active TSS	Brain Cingulate Gyrus	brain
42	chr19:19779200-19780400	Active TSS	Thymus	Thymus
43	chr19:19779200-19780600	Active TSS	Left Ventricle	heart
44	chr19:19779200-19780800	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr19:19779200-19780800	Active TSS	Fetal Intestine Small	intestine
46	chr19:19779200-19780800	Active TSS	HMEC	breast
47	chr19:19779200-19781000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr19:19779200-19781000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:19779200-19781200	Active TSS	Gastric	stomach
50	chr19:19779200-19781200	Active TSS	Small Intestine	intestine

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