Variant report

Variant	rs2296377
Chromosome Location	chr1:179051300-179051301
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:391)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:391 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr1:179050693-179051496	A549	lung:	n/a	chr1:179051125-179051134
2	POLR2A	chr1:179050648-179052242	MCF-7	breast:	n/a	n/a
3	YY1	chr1:179050780-179051596	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr1:179050421-179053208	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:179050569-179051625	U87	brain:	n/a	n/a
6	SIN3AK20	chr1:179050684-179052245	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr1:179050620-179052113	K562	blood:	n/a	n/a
8	MAX	chr1:179050667-179051337	HUVEC	blood vessel:	n/a	chr1:179050699-179050708
9	RCOR1	chr1:179050595-179051510	HepG2	liver:	n/a	n/a
10	TCF12	chr1:179050456-179052398	A549	lung:	n/a	n/a
11	TEAD4	chr1:179050389-179051453	K562	blood:	n/a	n/a
12	REST	chr1:179050757-179051563	A549	lung:	n/a	chr1:179051054-179051068 chr1:179051054-179051074
13	POLR2A	chr1:179050485-179052344	K562	blood:	n/a	n/a
14	MXI1	chr1:179050568-179052638	SK-N-SH	brain:	n/a	chr1:179051135-179051150
15	ZBTB7A	chr1:179050962-179051917	K562	blood:	n/a	chr1:179051582-179051593
16	POLR2A	chr1:179049925-179052426	GM12878	blood:	n/a	n/a
17	TAF1	chr1:179050831-179051343	Hela-S3	cervix:	n/a	n/a
18	MAZ	chr1:179050435-179052538	IMR90	lung:	n/a	chr1:179051658-179051668 chr1:179052196-179052205 chr1:179050699-179050708
19	FOSL2	chr1:179050471-179051311	HepG2	liver:	n/a	n/a
20	NFYA	chr1:179050941-179051307	K562	blood:	n/a	n/a
21	SPI1	chr1:179051041-179051317	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:179050547-179052186	Hela-S3	cervix:	n/a	n/a
23	ELF1	chr1:179050672-179051383	HepG2	liver:	n/a	chr1:179050813-179050824
24	GABPA	chr1:179050849-179051428	SK-N-SH	brain:	n/a	chr1:179051125-179051134
25	CCNT2	chr1:179050773-179051734	K562	blood:	n/a	n/a
26	POLR2A	chr1:179050648-179051510	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr1:179050676-179051430	K562	blood:	n/a	n/a
28	MTA3	chr1:179050015-179052498	GM12878	blood:	n/a	n/a
29	SIN3AK20	chr1:179050408-179052408	MCF-7	breast:	n/a	n/a
30	MAX	chr1:179050885-179051382	NB4	blood:	n/a	n/a
31	MAX	chr1:179050662-179051451	Hela-S3	cervix:	n/a	chr1:179050699-179050708
32	RELA	chr1:179050239-179051560	GM18951	blood:	n/a	chr1:179050571-179050580 chr1:179050571-179050580
33	USF1	chr1:179050937-179051304	H1-hESC	embryonic stem cell:	n/a	n/a
34	UBTF	chr1:179050649-179052011	K562	blood:	n/a	n/a
35	RUNX3	chr1:179049989-179051669	GM12878	blood:	n/a	n/a
36	YY1	chr1:179051064-179051387	HCT-116	colon:	n/a	n/a
37	RELA	chr1:179050164-179051395	GM10847	blood:	n/a	chr1:179050571-179050580 chr1:179050571-179050580
38	YY1	chr1:179051207-179051306	K562	blood:	n/a	n/a
39	ZNF143	chr1:179050550-179051452	GM12878	blood:	n/a	n/a
40	TBP	chr1:179050649-179051875	K562	blood:	n/a	n/a
41	MYC	chr1:179051107-179051366	NB4	blood:	n/a	n/a
42	EP300	chr1:179050544-179051473	GM12878	blood:	n/a	n/a
43	MYC	chr1:179050372-179052402	K562	blood:	n/a	chr1:179051658-179051668 chr1:179052196-179052205 chr1:179050699-179050708
44	MAX	chr1:179050568-179052474	HepG2	liver:	n/a	chr1:179051658-179051668 chr1:179052196-179052205 chr1:179050699-179050708
45	TCF12	chr1:179050812-179051328	GM12878	blood:	n/a	n/a
46	USF1	chr1:179050616-179051430	ECC-1	luminal epithelium:	n/a	n/a
47	KAP1	chr1:179050566-179051461	HEK293	kidney:	n/a	n/a
48	TAF1	chr1:179050615-179051463	MCF-7	breast:	n/a	n/a
49	NFYA	chr1:179050835-179051366	Hela-S3	cervix:	n/a	n/a
50	MAX	chr1:179050645-179052385	SK-N-SH	brain:	n/a	chr1:179051658-179051668 chr1:179052196-179052205 chr1:179050699-179050708

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:179051253-179051303	H1-hESC	embryonic stem cell:	embryo
2	chr1:179051253-179051303	NH-A	brain:	n/a
3	chr1:179051253-179051303	AoSMC	blood vessel:	n/a
4	chr1:179051253-179051303	GM12891	blood:	n/a
5	chr1:179051253-179051303	SK-N-SH_RA	brain:	n/a
6	chr1:179051253-179051303	HCM	heart:	n/a
7	chr1:179051253-179051303	PFSK-1	brain:	n/a
8	chr1:179051253-179051303	IMR90	lung:	fetal
9	chr1:179051253-179051303	HepG2	liver:	n/a
10	chr1:179051253-179051303	RPTEC	kidney:	n/a
11	chr1:179051253-179051303	AG09319	gingival:	n/a
12	chr1:179051253-179051303	NHDF-neo	bronchial:	n/a
13	chr1:179051253-179051303	MCF-7	breast:	n/a
14	chr1:179051253-179051303	Hepatocyte	liver:	n/a
15	chr1:179051253-179051303	T-47D	breast:	n/a
16	chr1:179051253-179051303	Jurkat	blood:	n/a
17	chr1:179051253-179051303	HAEpiC	amniotic membrane:	n/a
18	chr1:179051253-179051303	ECC-1	luminal epithelium:	n/a
19	chr1:179051253-179051303	Caco-2	colon:	n/a
20	chr1:179051253-179051303	BJ	skin:	n/a
21	chr1:179051253-179051303	SK-N-MC	brain:	n/a
22	chr1:179051253-179051303	HRPEpiC	eye:	n/a
23	chr1:179051253-179051303	ovcar-3	ovarian:	n/a
24	chr1:179051253-179051303	K562	blood:	n/a
25	chr1:179051253-179051303	NB4	blood:	n/a
26	chr1:179051253-179051303	HCPEpiC	choroid plexus:	n/a
27	chr1:179051253-179051303	U87	brain:	n/a
28	chr1:179051253-179051303	GM12892	blood:	n/a
29	chr1:179051253-179051303	HMEC	breast:	n/a
30	chr1:179051253-179051303	NHBE	bronchial:	n/a
31	chr1:179051253-179051303	LNCaP	prostate:	n/a
32	chr1:179051253-179051303	HL-60	blood:	n/a
33	chr1:179051253-179051303	Hela-S3	cervix:	n/a
34	chr1:179051253-179051303	HIPEpiC	eye:	n/a
35	chr1:179051253-179051303	HRCEpiC	kidney:	n/a
36	chr1:179051253-179051303	GM06990	blood:	n/a
37	chr1:179051253-179051303	HEEpiC	esophagus:	n/a
38	chr1:179051253-179051303	AG04449	skin:	fetal
39	chr1:179051253-179051303	GM19239	blood:	n/a
40	chr1:179051253-179051303	CMK	blood:	n/a
41	chr1:179051253-179051303	AG09309	skin:	n/a
42	chr1:179051253-179051303	PANC-1	pancreas:	n/a
43	chr1:179051253-179051303	GM12878	blood:	n/a
44	chr1:179051253-179051303	MCF10A-Er-Src	breast:	n/a
45	chr1:179051253-179051303	SKMC	muscle:	n/a
46	chr1:179051253-179051303	NT2-D1	testis:	n/a
47	chr1:179051253-179051303	SK-N-SH	brain:	n/a
48	chr1:179051253-179051303	AG04450	lung:	fetal
49	chr1:179051253-179051303	HNPCEpiC	eye:	n/a
50	chr1:179051253-179051303	HCT-116	colon:	n/a

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:31845479..31846009-chr1:179050951..179051607,2	Hela-S3	cervix:
2	chr1:179049954..179052769-chr1:179333565..179337813,7	MCF-7	breast:
3	chr1:179050855..179052664-chr1:179261724..179264711,2	K562	blood:
4	chr1:179050855..179053575-chr1:179263211..179266215,3	K562	blood:
5	chr1:178837797..178839494-chr1:179049948..179052882,2	K562	blood:
6	chr1:178993182..178999783-chr1:179045102..179052535,14	MCF-7	breast:
7	chr1:179048972..179052099-chr1:179331450..179336701,5	MCF-7	breast:
8	chr1:179049424..179053663-chr1:179259743..179264339,5	MCF-7	breast:
9	chr1:179049160..179052033-chr1:179333339..179335895,3	K562	blood:
10	chr1:178994647..178996585-chr1:179051040..179053373,3	MCF-7	breast:

No data

Variant related genes	Relation type
TOR3A	TF binding region
TOR3A	CpG island
ENSG00000057252	Chromatin interaction
ENSG00000116199	Chromatin interaction
ENSG00000263633	Chromatin interaction
ENSG00000162779	Chromatin interaction
ENSG00000121769	Chromatin interaction
ENSG00000116194	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10082052	0.89[AMR][1000 genomes]
rs10458367	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1046385	0.87[GIH][hapmap]
rs10913691	0.85[AMR][1000 genomes]
rs1325194	0.83[AMR][1000 genomes]
rs17362081	0.83[AMR][1000 genomes]
rs2636290	0.83[AMR][1000 genomes]
rs3813638	0.81[CHB][hapmap]
rs3818433	0.83[AMR][1000 genomes]
rs4360489	0.82[AMR][1000 genomes]
rs4651014	0.83[AMR][1000 genomes]
rs4652344	0.80[AMR][1000 genomes]
rs4652348	0.86[AMR][1000 genomes]
rs6425512	0.81[CHB][hapmap];0.82[GIH][hapmap];0.83[AMR][1000 genomes]
rs6697029	0.82[AMR][1000 genomes]
rs7532578	0.80[AMR][1000 genomes]
rs7538498	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7544801	0.81[CHB][hapmap];0.85[GIH][hapmap];0.83[AMR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2296377	TOR3A	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179050200-179052400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:179050200-179052400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr1:179050200-179052600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:179050400-179052000	Active TSS	Psoas Muscle	Psoas
5	chr1:179050400-179052000	Active TSS	HepG2	liver
6	chr1:179050400-179052400	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr1:179050400-179053000	Active TSS	H9 Cell Line	embryonic stem cell
8	chr1:179050600-179051400	Active TSS	Colonic Mucosa	Colon
9	chr1:179050600-179051800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:179050600-179051800	Active TSS	Fetal Brain Female	brain
11	chr1:179050600-179052000	Active TSS	Colon Smooth Muscle	Colon
12	chr1:179050600-179052000	Active TSS	Esophagus	oesophagus
13	chr1:179050600-179052000	Active TSS	Left Ventricle	heart
14	chr1:179050600-179052200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:179050600-179052200	Active TSS	Aorta	Aorta
16	chr1:179050600-179052200	Active TSS	Fetal Intestine Large	intestine
17	chr1:179050600-179052200	Active TSS	Ovary	ovary
18	chr1:179050600-179052200	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr1:179050600-179052200	Active TSS	Small Intestine	intestine
20	chr1:179050600-179052400	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr1:179050600-179052400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:179050600-179052400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:179050600-179052600	Active TSS	NHLF	lung
24	chr1:179050800-179051800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:179050800-179051800	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr1:179050800-179051800	Active TSS	Liver	Liver
27	chr1:179050800-179051800	Active TSS	Brain Anterior Caudate	brain
28	chr1:179050800-179051800	Active TSS	Brain Hippocampus Middle	brain
29	chr1:179050800-179051800	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr1:179050800-179051800	Active TSS	Spleen	Spleen
31	chr1:179050800-179051800	Active TSS	Monocytes-CD14+_RO01746	blood
32	chr1:179050800-179052000	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr1:179050800-179052000	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr1:179050800-179052000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr1:179050800-179052000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:179050800-179052000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:179050800-179052000	Active TSS	Fetal Intestine Small	intestine
38	chr1:179050800-179052000	Active TSS	Gastric	stomach
39	chr1:179050800-179052000	Active TSS	Pancreas	Pancrea
40	chr1:179050800-179052000	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr1:179050800-179052000	Active TSS	Right Atrium	heart
42	chr1:179050800-179052000	Active TSS	Right Ventricle	heart
43	chr1:179050800-179052000	Active TSS	Stomach Mucosa	stomach
44	chr1:179050800-179052000	Active TSS	Thymus	Thymus
45	chr1:179050800-179052200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:179050800-179052200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:179050800-179052200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:179050800-179052200	Active TSS	Brain Substantia Nigra	brain
49	chr1:179050800-179052200	Active TSS	Rectal Smooth Muscle	rectum
50	chr1:179050800-179052400	Active TSS	Placenta Amnion	Placenta Amnion

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