Variant report

Variant	rs28991583
Chromosome Location	chr1:179199007-179199008
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	TAF1	chr1:179198051-179199154	HepG2	liver:	n/a	n/a
2	SMARCB1	chr1:179197960-179199297	Hela-S3	cervix:	n/a	n/a
3	MAX	chr1:179198376-179199385	MCF-7	breast:	n/a	chr1:179199191-179199198
4	YY1	chr1:179198926-179199285	K562	blood:	n/a	n/a
5	YY1	chr1:179198172-179199261	SK-N-SH	brain:	n/a	chr1:179198587-179198601 chr1:179198794-179198811 chr1:179198554-179198563 chr1:179198228-179198248 chr1:179198201-179198212 chr1:179198669-179198683 chr1:179198689-179198700 chr1:179198229-179198248 chr1:179198654-179198668
6	POLR2A	chr1:179198851-179199203	A549	lung:	n/a	n/a
7	POLR2A	chr1:179198924-179199222	GM12892	blood:	n/a	n/a
8	POLR2A	chr1:179198324-179199341	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr1:179198511-179199220	K562	blood:	n/a	n/a
10	SIN3A	chr1:179197840-179199404	H1-hESC	embryonic stem cell:	n/a	chr1:179198604-179198613
11	MYC	chr1:179198066-179200154	K562	blood:	n/a	chr1:179199609-179199619 chr1:179198329-179198339 chr1:179199610-179199617 chr1:179199607-179199620 chr1:179199609-179199618 chr1:179198198-179198208 chr1:179199608-179199618 chr1:179199605-179199620 chr1:179199191-179199198 chr1:179199610-179199619 chr1:179199607-179199622 chr1:179199608-179199619
12	POLR2A	chr1:179198908-179199242	SK-N-SH	brain:	n/a	n/a
13	HDAC2	chr1:179198954-179199326	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAZ	chr1:179197859-179199300	Hela-S3	cervix:	n/a	chr1:179198329-179198339 chr1:179198198-179198208 chr1:179199191-179199198
15	TCF12	chr1:179198855-179199481	A549	lung:	n/a	chr1:179199042-179199049
16	POLR2A	chr1:179198402-179199210	HepG2	liver:	n/a	n/a
17	ZEB1	chr1:179198973-179199241	GM12878	blood:	n/a	n/a
18	ZEB1	chr1:179198314-179199469	HepG2	liver:	n/a	n/a
19	POLR2A	chr1:179198605-179199082	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr1:179198390-179199189	A549	lung:	n/a	n/a
21	E2F6	chr1:179198936-179199456	H1-hESC	embryonic stem cell:	n/a	n/a
22	YY1	chr1:179198377-179199166	SK-N-SH_RA	brain:	n/a	chr1:179198587-179198601 chr1:179198794-179198811 chr1:179198554-179198563 chr1:179198669-179198683 chr1:179198689-179198700 chr1:179198654-179198668
23	SIN3AK20	chr1:179198947-179199129	HepG2	liver:	n/a	n/a
24	UBTF	chr1:179197783-179199168	K562	blood:	n/a	n/a
25	MAX	chr1:179197942-179199881	HCT-116	colon:	n/a	chr1:179199609-179199619 chr1:179198329-179198339 chr1:179199610-179199617 chr1:179199607-179199620 chr1:179199609-179199618 chr1:179198198-179198208 chr1:179199608-179199618 chr1:179199605-179199620 chr1:179199191-179199198 chr1:179199610-179199619 chr1:179199607-179199622 chr1:179199608-179199619
26	POLR2A	chr1:179198099-179199311	Raji	blood:	n/a	n/a
27	MAX	chr1:179198690-179199848	SK-N-SH	brain:	n/a	chr1:179199609-179199619 chr1:179199610-179199617 chr1:179199607-179199620 chr1:179199609-179199618 chr1:179199608-179199618 chr1:179199605-179199620 chr1:179199191-179199198 chr1:179199610-179199619 chr1:179199607-179199622 chr1:179199608-179199619
28	POLR2A	chr1:179198859-179199209	A549	lung:	n/a	n/a
29	TAF1	chr1:179198946-179199272	SK-N-SH	brain:	n/a	n/a
30	MAX	chr1:179199007-179199313	GM12878	blood:	n/a	chr1:179199191-179199198
31	POLR2A	chr1:179198953-179199279	HCT-116	colon:	n/a	n/a
32	MXI1	chr1:179197473-179200615	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr1:179198167-179199291	MCF-7	breast:	n/a	n/a
34	MXI1	chr1:179198120-179199366	HepG2	liver:	n/a	n/a
35	EP300	chr1:179198384-179199010	ECC-1	luminal epithelium:	n/a	chr1:179198684-179198700
36	POLR2A	chr1:179198858-179199242	A549	lung:	n/a	n/a
37	POLR2A	chr1:179198895-179199314	ECC-1	luminal epithelium:	n/a	n/a
38	ZBTB7A	chr1:179198333-179199443	ECC-1	luminal epithelium:	n/a	chr1:179198757-179198766
39	CHD2	chr1:179198953-179199173	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAX	chr1:179197803-179199334	HepG2	liver:	n/a	chr1:179198329-179198339 chr1:179198198-179198208 chr1:179199191-179199198
41	MAX	chr1:179198861-179199367	K562	blood:	n/a	chr1:179199191-179199198
42	MAX	chr1:179198519-179199509	ECC-1	luminal epithelium:	n/a	chr1:179199191-179199198
43	POLR2A	chr1:179198388-179199181	GM18951	blood:	n/a	n/a
44	POLR2A	chr1:179198926-179199168	Hela-S3	cervix:	n/a	n/a
45	MAX	chr1:179198748-179199915	SK-N-SH	brain:	n/a	chr1:179199609-179199619 chr1:179199610-179199617 chr1:179199607-179199620 chr1:179199609-179199618 chr1:179199608-179199618 chr1:179199605-179199620 chr1:179199191-179199198 chr1:179199610-179199619 chr1:179199607-179199622 chr1:179199608-179199619
46	E2F6	chr1:179198930-179199402	H1-hESC	embryonic stem cell:	n/a	n/a
47	YY1	chr1:179198969-179199354	GM12878	blood:	n/a	n/a
48	EGR1	chr1:179198856-179199155	K562	blood:	n/a	chr1:179199054-179199069 chr1:179198879-179198893 chr1:179199055-179199068
49	POLR2A	chr1:179198340-179199287	H1-neurons	neurons:	n/a	n/a
50	POLR2A	chr1:179198976-179199233	MCF-7	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:179198964-179199014	GM12891	blood:	n/a
2	chr1:179198964-179199014	NH-A	brain:	n/a
3	chr1:179198964-179199014	HCM	heart:	n/a
4	chr1:179198964-179199014	AG10803	skin:	n/a
5	chr1:179198964-179199014	MCF-7	breast:	n/a
6	chr1:179198964-179199014	PFSK-1	brain:	n/a
7	chr1:179198964-179199014	H1-hESC	embryonic stem cell:	embryo
8	chr1:179198964-179199014	HEEpiC	esophagus:	n/a
9	chr1:179198964-179199014	MCF10A-Er-Src	breast:	n/a
10	chr1:179198964-179199014	GM12878	blood:	n/a
11	chr1:179198964-179199014	AG09319	gingival:	n/a
12	chr1:179198964-179199014	HL-60	blood:	n/a
13	chr1:179198964-179199014	PANC-1	pancreas:	n/a
14	chr1:179198964-179199014	BJ	skin:	n/a
15	chr1:179198964-179199014	SK-N-MC	brain:	n/a
16	chr1:179198964-179199014	ovcar-3	ovarian:	n/a
17	chr1:179198964-179199014	Jurkat	blood:	n/a
18	chr1:179198964-179199014	NB4	blood:	n/a
19	chr1:179198964-179199014	Hepatocyte	liver:	n/a
20	chr1:179198964-179199014	HCT-116	colon:	n/a
21	chr1:179198964-179199014	AG09309	skin:	n/a
22	chr1:179198964-179199014	HEK293	kidney:	embryo
23	chr1:179198964-179199014	HRE	kidney:	n/a
24	chr1:179198964-179199014	ECC-1	luminal epithelium:	n/a
25	chr1:179198964-179199014	HRCEpiC	kidney:	n/a
26	chr1:179198964-179199014	HCF	heart:	n/a
27	chr1:179198964-179199014	HIPEpiC	eye:	n/a
28	chr1:179198964-179199014	GM19239	blood:	n/a
29	chr1:179198964-179199014	U87	brain:	n/a
30	chr1:179198964-179199014	GM12892	blood:	n/a
31	chr1:179198964-179199014	HPAEpiC	pulmonary alveolar:	n/a
32	chr1:179198964-179199014	HepG2	liver:	n/a
33	chr1:179198964-179199014	RPTEC	kidney:	n/a
34	chr1:179198964-179199014	ProgFib	skin:	n/a
35	chr1:179198964-179199014	BE2_C	brain:	n/a
36	chr1:179198964-179199014	HRPEpiC	eye:	n/a
37	chr1:179198964-179199014	SAEC	small airway:	n/a
38	chr1:179198964-179199014	NHBE	bronchial:	n/a
39	chr1:179198964-179199014	HMEC	breast:	n/a
40	chr1:179198964-179199014	PrEC	prostate:	n/a
41	chr1:179198964-179199014	HNPCEpiC	eye:	n/a
42	chr1:179198964-179199014	AG04449	skin:	fetal
43	chr1:179198964-179199014	GM06990	blood:	n/a
44	chr1:179198964-179199014	NHDF-neo	bronchial:	n/a
45	chr1:179198964-179199014	Caco-2	colon:	n/a
46	chr1:179198964-179199014	SK-N-SH_RA	brain:	n/a
47	chr1:179198964-179199014	Hela-S3	cervix:	n/a
48	chr1:179198964-179199014	AoSMC	blood vessel:	n/a
49	chr1:179198964-179199014	HCPEpiC	choroid plexus:	n/a
50	chr1:179198964-179199014	HAEpiC	amniotic membrane:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:179198544..179200421-chr1:179334252..179336417,2	MCF-7	breast:
2	chr1:179189295..179193775-chr1:179196197..179201101,5	K562	blood:
3	chr1:179188599..179190144-chr1:179197953..179200570,2	MCF-7	breast:
4	chr1:179168461..179170793-chr1:179198127..179200126,2	MCF-7	breast:
5	chr1:179187242..179191261-chr1:179196503..179201085,5	MCF-7	breast:

Variant related genes	Relation type
ABL2	TF binding region
ABL2	CpG island
ENSG00000225711	Chromatin interaction
ENSG00000162779	Chromatin interaction
ENSG00000201619	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11799509	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801262	1.00[ASN][1000 genomes]
rs11802142	1.00[ASN][1000 genomes]
rs11802378	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11804174	1.00[ASN][1000 genomes]
rs11807230	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807239	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807253	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11809032	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811569	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811579	0.96[EUR][1000 genomes]
rs2636273	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2816182	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28913876	1.00[ASN][1000 genomes]
rs28913894	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28914473	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28991582	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28991584	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72707289	1.00[ASN][1000 genomes]
rs72707290	1.00[ASN][1000 genomes]
rs72707297	1.00[ASN][1000 genomes]
rs72709407	1.00[ASN][1000 genomes]
rs72709410	1.00[ASN][1000 genomes]
rs72709411	1.00[ASN][1000 genomes]
rs72709420	1.00[ASN][1000 genomes]
rs72709430	1.00[ASN][1000 genomes]
rs72709434	1.00[ASN][1000 genomes]
rs72709443	1.00[ASN][1000 genomes]
rs72709451	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709459	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709462	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709463	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709464	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709467	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709474	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709475	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709476	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709477	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709479	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709481	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709485	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709486	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709487	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709488	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709490	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709492	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709493	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709494	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709495	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709496	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709497	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709498	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711608	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711609	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711612	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711614	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711615	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713484	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713485	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713494	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713501	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72715506	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72715515	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72715520	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72715533	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72715595	1.00[ASN][1000 genomes]
rs72715597	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72715599	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv3441716	chr1:179197554-179200302	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 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	chr1:179197400-179199400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:179197600-179199400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:179197600-179199400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:179197600-179199400	Active TSS	Aorta	Aorta
5	chr1:179197600-179199400	Active TSS	Right Atrium	heart
6	chr1:179197600-179199800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:179197600-179199800	Active TSS	NHLF	lung
8	chr1:179197800-179199200	Active TSS	Fetal Intestine Large	intestine
9	chr1:179197800-179199400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr1:179197800-179199400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:179197800-179199400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:179197800-179199400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:179197800-179199400	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr1:179197800-179199400	Active TSS	Esophagus	oesophagus
15	chr1:179197800-179199400	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr1:179197800-179199400	Active TSS	Placenta	Placenta
17	chr1:179197800-179199400	Active TSS	Left Ventricle	heart
18	chr1:179197800-179199400	Active TSS	Ovary	ovary
19	chr1:179197800-179199400	Active TSS	Psoas Muscle	Psoas
20	chr1:179197800-179199400	Active TSS	A549	lung
21	chr1:179197800-179199600	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr1:179198000-179199200	Active TSS	H1 Cell Line	embryonic stem cell
23	chr1:179198000-179199200	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr1:179198000-179199200	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr1:179198000-179199200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:179198000-179199200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:179198000-179199200	Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr1:179198000-179199200	Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr1:179198000-179199200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:179198000-179199200	Active TSS	Brain Hippocampus Middle	brain
31	chr1:179198000-179199200	Active TSS	Brain Substantia Nigra	brain
32	chr1:179198000-179199200	Active TSS	Sigmoid Colon	Sigmoid Colon
33	chr1:179198000-179199200	Active TSS	Spleen	Spleen
34	chr1:179198000-179199200	Active TSS	Hela-S3	cervix
35	chr1:179198000-179199200	Active TSS	HepG2	liver
36	chr1:179198000-179199200	Active TSS	K562	blood
37	chr1:179198000-179199200	Active TSS	Osteobl	bone
38	chr1:179198000-179199400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:179198000-179199400	Active TSS	H9 Cell Line	embryonic stem cell
40	chr1:179198000-179199400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:179198000-179199400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:179198000-179199400	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr1:179198000-179199400	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr1:179198000-179199400	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr1:179198000-179199400	Active TSS	Colon Smooth Muscle	Colon
46	chr1:179198000-179199400	Active TSS	Fetal Brain Female	brain
47	chr1:179198000-179199400	Active TSS	Fetal Kidney	kidney
48	chr1:179198000-179199400	Active TSS	Fetal Stomach	stomach
49	chr1:179198000-179199400	Active TSS	Gastric	stomach
50	chr1:179198000-179199400	Active TSS	Small Intestine	intestine

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