Variant report

Variant	rs2493119
Chromosome Location	chr1:179263356-179263357
allele	C/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	MYC	chr1:179262740-179263495	MCF10A-Er-Src	breast:	n/a	chr1:179262899-179262909
2	POLR2A	chr1:179262550-179263472	GM12878	blood:	n/a	n/a
3	CREB1	chr1:179262448-179263400	HepG2	liver:	n/a	n/a
4	E2F6	chr1:179262454-179263435	K562	blood:	n/a	chr1:179263100-179263111 chr1:179263241-179263248 chr1:179263241-179263248 chr1:179263237-179263249 chr1:179263240-179263248 chr1:179263241-179263248
5	SIN3AK20	chr1:179262283-179263621	MCF-7	breast:	n/a	n/a
6	EP300	chr1:179262714-179263364	ECC-1	luminal epithelium:	n/a	chr1:179263049-179263065 chr1:179263048-179263064
7	BRCA1	chr1:179262419-179263555	Hela-S3	cervix:	n/a	n/a
8	IRF1	chr1:179262581-179263622	K562	blood:	n/a	chr1:179263385-179263398 chr1:179262805-179262819 chr1:179262817-179262831 chr1:179263380-179263392 chr1:179263540-179263552 chr1:179263379-179263393 chr1:179263380-179263392 chr1:179263385-179263398 chr1:179263541-179263551 chr1:179263380-179263394 chr1:179263379-179263392 chr1:179263380-179263393 chr1:179263382-179263393 chr1:179263538-179263552 chr1:179263539-179263553 chr1:179263381-179263395 chr1:179263541-179263555 chr1:179263380-179263394 chr1:179263381-179263392 chr1:179263383-179263393 chr1:179263537-179263551 chr1:179263379-179263399 chr1:179263380-179263397 chr1:179263384-179263398 chr1:179263385-179263398
9	SIN3A	chr1:179262504-179263486	GM12878	blood:	n/a	n/a
10	MAX	chr1:179262290-179263557	A549	lung:	n/a	chr1:179262899-179262909
11	CBX3	chr1:179262230-179263508	K562	blood:	n/a	n/a
12	MAX	chr1:179262401-179263473	K562	blood:	n/a	chr1:179262899-179262909
13	MAX	chr1:179262201-179263519	MCF-7	breast:	n/a	chr1:179262899-179262909
14	CEBPB	chr1:179263332-179264090	K562	blood:	n/a	chr1:179263722-179263733
15	NFIC	chr1:179262905-179263395	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:179262514-179263364	SK-N-MC	brain:	n/a	n/a
17	CHD1	chr1:179262939-179263537	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr1:179262449-179263410	Hela-S3	cervix:	n/a	n/a
19	NFIC	chr1:179262337-179263365	ECC-1	luminal epithelium:	n/a	chr1:179262745-179262761 chr1:179262745-179262762
20	SIN3AK20	chr1:179262484-179263475	A549	lung:	n/a	n/a
21	TCF7L2	chr1:179262444-179264298	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr1:179262420-179263375	HepG2	liver:	n/a	n/a
23	POLR2A	chr1:179262525-179263434	Raji	blood:	n/a	n/a
24	CREB1	chr1:179262455-179263465	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:179262524-179263399	GM15510	blood:	n/a	n/a
26	POLR2A	chr1:179262516-179263592	IMR90	lung:	n/a	n/a
27	MYC	chr1:179262387-179263485	K562	blood:	n/a	chr1:179262899-179262909
28	CHD2	chr1:179262627-179263362	HepG2	liver:	n/a	chr1:179262807-179262817
29	MAX	chr1:179262617-179263621	ECC-1	luminal epithelium:	n/a	chr1:179262899-179262909
30	POLR2A	chr1:179262520-179263365	GM18505	blood:	n/a	n/a
31	MXI1	chr1:179262398-179263434	HepG2	liver:	n/a	n/a
32	POLR2A	chr1:179262526-179263372	GM18526	blood:	n/a	n/a
33	MAX	chr1:179262377-179263407	HepG2	liver:	n/a	chr1:179262899-179262909
34	POLR2A	chr1:179262543-179263378	GM12892	blood:	n/a	n/a
35	POLR2A	chr1:179262588-179263384	Hela-S3	cervix:	n/a	n/a
36	MAX	chr1:179263227-179263427	H1-hESC	embryonic stem cell:	n/a	n/a
37	MAX	chr1:179262470-179264442	Hela-S3	cervix:	n/a	chr1:179262899-179262909 chr1:179264205-179264212
38	CHD2	chr1:179263009-179263451	K562	blood:	n/a	n/a
39	SIN3AK20	chr1:179262801-179263432	PFSK-1	brain:	n/a	n/a
40	POLR2A	chr1:179262449-179263460	H1-hESC	embryonic stem cell:	n/a	n/a
41	MAX	chr1:179262351-179263573	HepG2	liver:	n/a	chr1:179262899-179262909
42	RCOR1	chr1:179262441-179264319	Hela-S3	cervix:	n/a	n/a
43	SMC3	chr1:179262462-179263493	Hela-S3	cervix:	n/a	n/a
44	ZNF263	chr1:179262483-179263463	HEK293-T-REx	kidney:	n/a	n/a
45	E2F6	chr1:179262586-179263437	A549	lung:	n/a	chr1:179263100-179263111 chr1:179263241-179263248 chr1:179263241-179263248 chr1:179263237-179263249 chr1:179263240-179263248 chr1:179263241-179263248
46	CEBPB	chr1:179263165-179263777	MCF-7	breast:	n/a	chr1:179263722-179263733
47	E2F4	chr1:179262536-179263403	K562	blood:	n/a	chr1:179263241-179263248 chr1:179263241-179263248 chr1:179263237-179263249 chr1:179263240-179263248 chr1:179263241-179263248
48	SPI1	chr1:179263096-179263564	HL-60	blood:	n/a	n/a
49	SIN3AK20	chr1:179262454-179263389	PANC-1	pancreas:	n/a	n/a
50	MAX	chr1:179262497-179263462	H1-hESC	embryonic stem cell:	n/a	chr1:179262899-179262909

No.	Distal block	Cell Line	Cell type
1	chr1:179262860..179263465-chr11:77531402..77532037,2	Hela-S3	cervix:
2	chr1:179260885..179265137-chr1:179333383..179339387,7	MCF-7	breast:
3	chr1:179049424..179053663-chr1:179259743..179264339,5	MCF-7	breast:
4	chr1:179050855..179052664-chr1:179261724..179264711,2	K562	blood:
5	chr1:179050855..179053575-chr1:179263211..179266215,3	K562	blood:
6	chr1:179110656..179113275-chr1:179262488..179264481,2	K562	blood:

Variant related genes	Relation type
SOAT1	TF binding region
ENSG00000048649	Chromatin interaction
ENSG00000143322	Chromatin interaction
ENSG00000263633	Chromatin interaction
ENSG00000186283	Chromatin interaction
ENSG00000162779	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1034269	0.81[CHB][hapmap]
rs10798655	0.89[ASN][1000 genomes]
rs10798656	0.81[CHB][hapmap]
rs10913714	0.81[CHB][hapmap]
rs10913718	0.81[CHB][hapmap]
rs12047131	0.81[CHB][hapmap]
rs12138973	0.80[ASN][1000 genomes]
rs12725375	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12749666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1475799	0.81[CHB][hapmap]
rs17368880	0.81[CHB][hapmap]
rs2050450	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2050451	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2152318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2247061	0.96[ASN][1000 genomes]
rs2248979	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2250352	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2250477	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2254214	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2254580	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2254623	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255375	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs2257089	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2257100	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2484440	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2484443	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2484446	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2492777	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2492778	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2493116	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2493117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2493118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2783391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2783392	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2783393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2902276	0.81[CHB][hapmap]
rs404818	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs433722	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4652364	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56371666	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61824366	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6425530	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6698438	0.81[CHB][hapmap]
rs6699698	0.81[CHB][hapmap]
rs7523431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7532172	0.81[CHB][hapmap]
rs7543894	0.81[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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	chr1:179261800-179265800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:179262000-179264200	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr1:179262200-179263800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:179262200-179263800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr1:179262200-179263800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:179262200-179264200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr1:179262200-179264200	Active TSS	Fetal Brain Female	brain
8	chr1:179262200-179264400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr1:179262200-179264400	Active TSS	HSMM	muscle
10	chr1:179262200-179264800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr1:179262400-179263400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:179262400-179263400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:179262400-179263400	Active TSS	H9 Cell Line	embryonic stem cell
14	chr1:179262400-179263400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:179262400-179263400	Active TSS	Esophagus	oesophagus
16	chr1:179262400-179263600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:179262400-179263600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:179262400-179263600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:179262400-179263600	Active TSS	Fetal Lung	lung
20	chr1:179262400-179263600	Active TSS	Fetal Thymus	thymus
21	chr1:179262400-179263800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr1:179262400-179263800	Active TSS	Fetal Intestine Small	intestine
23	chr1:179262400-179263800	Active TSS	Lung	lung
24	chr1:179262400-179264000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:179262400-179264000	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr1:179262400-179264000	Active TSS	Brain Cingulate Gyrus	brain
27	chr1:179262400-179264000	Active TSS	Brain Hippocampus Middle	brain
28	chr1:179262400-179264000	Active TSS	Stomach Mucosa	stomach
29	chr1:179262400-179264000	Flanking Active TSS	Thymus	Thymus
30	chr1:179262400-179264000	Active TSS	HSMMtube	muscle
31	chr1:179262400-179264200	Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr1:179262400-179264200	Active TSS	Brain Substantia Nigra	brain
33	chr1:179262400-179264200	Active TSS	Colon Smooth Muscle	Colon
34	chr1:179262400-179264200	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr1:179262400-179264200	Active TSS	Rectal Smooth Muscle	rectum
36	chr1:179262400-179264200	Active TSS	Right Atrium	heart
37	chr1:179262400-179264200	Active TSS	Right Ventricle	heart
38	chr1:179262400-179264200	Active TSS	GM12878-XiMat	blood
39	chr1:179262400-179264200	Active TSS	Osteobl	bone
40	chr1:179262400-179264400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
41	chr1:179262400-179264400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:179262400-179264400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:179262400-179264400	Active TSS	Left Ventricle	heart
44	chr1:179262400-179264400	Active TSS	Ovary	ovary
45	chr1:179262400-179264600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:179262400-179264600	Active TSS	Brain Germinal Matrix	brain
47	chr1:179262400-179264600	Active TSS	Pancreas	Pancrea
48	chr1:179262400-179264600	Active TSS	Psoas Muscle	Psoas
49	chr1:179262400-179264800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
50	chr1:179262400-179264800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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