Variant report

Variant	rs7980483
Chromosome Location	chr12:59314407-59314408
allele	A/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	SP1	chr12:59313994-59314656	A549	lung:	n/a	chr12:59314366-59314387
2	RCOR1	chr12:59313843-59314704	HepG2	liver:	n/a	n/a
3	BACH1	chr12:59313457-59314573	H1-hESC	embryonic stem cell:	n/a	n/a
4	MYC	chr12:59313059-59314590	Hela-S3	cervix:	n/a	chr12:59313589-59313604 chr12:59314410-59314419 chr12:59313591-59313600 chr12:59313592-59313599 chr12:59314408-59314421 chr12:59313590-59313601 chr12:59314409-59314420 chr12:59313590-59313601 chr12:59314410-59314419
5	FOS	chr12:59314297-59314580	MCF10A-Er-Src	breast:	n/a	chr12:59314350-59314359 chr12:59314566-59314575
6	POLR2A	chr12:59313774-59314486	A549	lung:	n/a	n/a
7	USF2	chr12:59314173-59314599	HepG2	liver:	n/a	chr12:59314427-59314443 chr12:59314382-59314398 chr12:59314408-59314419
8	NFIC	chr12:59313891-59314793	ECC-1	luminal epithelium:	n/a	n/a
9	MXI1	chr12:59312927-59314729	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr12:59313244-59314650	H1-hESC	embryonic stem cell:	n/a	n/a
11	E2F6	chr12:59313149-59314852	H1-hESC	embryonic stem cell:	n/a	chr12:59313711-59313720 chr12:59314368-59314382
12	USF1	chr12:59314126-59314661	A549	lung:	n/a	chr12:59314409-59314420 chr12:59314427-59314443 chr12:59314382-59314398
13	HDAC2	chr12:59313294-59314623	MCF-7	breast:	n/a	chr12:59314118-59314127 chr12:59314060-59314069
14	USF2	chr12:59314254-59314766	GM12878	blood:	n/a	chr12:59314427-59314443 chr12:59314382-59314398 chr12:59314408-59314419
15	POLR2A	chr12:59314080-59314507	HepG2	liver:	n/a	n/a
16	MYC	chr12:59314404-59314412	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr12:59313766-59314512	HepG2	liver:	n/a	n/a
18	MAX	chr12:59313939-59314599	HUVEC	blood vessel:	n/a	chr12:59314410-59314419 chr12:59314408-59314421 chr12:59314409-59314420 chr12:59314410-59314419
19	TAF1	chr12:59313640-59314472	H1-hESC	embryonic stem cell:	n/a	n/a
20	USF1	chr12:59314238-59314533	HepG2	liver:	n/a	chr12:59314409-59314420 chr12:59314427-59314443 chr12:59314382-59314398
21	POLR2A	chr12:59313612-59314625	MCF-7	breast:	n/a	n/a
22	TCF12	chr12:59313833-59314837	ECC-1	luminal epithelium:	n/a	chr12:59314210-59314217
23	USF1	chr12:59314140-59314694	SK-N-SH	brain:	n/a	chr12:59314409-59314420 chr12:59314427-59314443 chr12:59314382-59314398
24	ZKSCAN1	chr12:59313860-59314748	Hela-S3	cervix:	n/a	n/a
25	TCF7L2	chr12:59313351-59314648	PANC-1	pancreas:	n/a	n/a
26	POLR2A	chr12:59313091-59314597	HUVEC	blood vessel:	n/a	n/a
27	E2F4	chr12:59313684-59314976	MCF10A-Er-Src	breast:	n/a	chr12:59313711-59313720 chr12:59314368-59314382
28	SIN3AK20	chr12:59314311-59314552	PANC-1	pancreas:	n/a	n/a
29	MAX	chr12:59314053-59314536	GM12878	blood:	n/a	chr12:59314410-59314419 chr12:59314408-59314421 chr12:59314409-59314420 chr12:59314410-59314419
30	NFIC	chr12:59314089-59314461	HepG2	liver:	n/a	n/a
31	MAZ	chr12:59313373-59314775	IMR90	lung:	n/a	chr12:59313589-59313604 chr12:59314410-59314419 chr12:59313591-59313600 chr12:59313592-59313599 chr12:59314408-59314421 chr12:59313590-59313601 chr12:59314409-59314420 chr12:59313590-59313601 chr12:59314410-59314419
32	NFYB	chr12:59314226-59314547	GM12878	blood:	n/a	chr12:59314373-59314388 chr12:59314373-59314388 chr12:59314374-59314388 chr12:59314375-59314390
33	POLR2A	chr12:59312997-59314638	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr12:59314146-59314435	HepG2	liver:	n/a	n/a
35	MAX	chr12:59313912-59314647	SK-N-SH	brain:	n/a	chr12:59314410-59314419 chr12:59314408-59314421 chr12:59314409-59314420 chr12:59314410-59314419
36	USF1	chr12:59313976-59314861	HCT-116	colon:	n/a	chr12:59314409-59314420 chr12:59314427-59314443 chr12:59314382-59314398
37	YY1	chr12:59314054-59314500	GM12878	blood:	n/a	n/a
38	POLR2A	chr12:59313006-59314615	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr12:59313106-59314544	GM18505	blood:	n/a	n/a
40	RFX5	chr12:59314004-59314457	HepG2	liver:	n/a	n/a
41	FOS	chr12:59314271-59314435	MCF10A-Er-Src	breast:	n/a	chr12:59314350-59314359
42	MAX	chr12:59313222-59314799	HCT-116	colon:	n/a	chr12:59313589-59313604 chr12:59314410-59314419 chr12:59313591-59313600 chr12:59313592-59313599 chr12:59314408-59314421 chr12:59313590-59313601 chr12:59314409-59314420 chr12:59313590-59313601 chr12:59314410-59314419
43	USF1	chr12:59314043-59314685	A549	lung:	n/a	chr12:59314409-59314420 chr12:59314427-59314443 chr12:59314382-59314398
44	MXI1	chr12:59312803-59315453	IMR90	lung:	n/a	n/a
45	TAF1	chr12:59313904-59314530	H1-hESC	embryonic stem cell:	n/a	n/a
46	TBL1XR1	chr12:59314330-59314491	GM12878	blood:	n/a	n/a
47	POLR2A	chr12:59314182-59314457	A549	lung:	n/a	n/a
48	E2F1	chr12:59313781-59314597	Hela-S3	cervix:	n/a	chr12:59314368-59314382
49	USF1	chr12:59314208-59314624	SK-N-SH_RA	brain:	n/a	chr12:59314409-59314420 chr12:59314427-59314443 chr12:59314382-59314398
50	ZNF143	chr12:59313985-59314574	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:59314400-59314450	H1-hESC	embryonic stem cell:	embryo
2	chr12:59314400-59314450	HAEpiC	amniotic membrane:	n/a
3	chr12:59314400-59314450	GM12878	blood:	n/a
4	chr12:59314400-59314450	GM06990	blood:	n/a
5	chr12:59314400-59314450	NHBE	bronchial:	n/a
6	chr12:59314400-59314450	HRCEpiC	kidney:	n/a
7	chr12:59314400-59314450	SKMC	muscle:	n/a
8	chr12:59314400-59314450	SK-N-SH	brain:	n/a
9	chr12:59314400-59314450	NHDF-neo	bronchial:	n/a
10	chr12:59314400-59314450	K562	blood:	n/a
11	chr12:59314400-59314450	GM12892	blood:	n/a
12	chr12:59314400-59314450	SAEC	small airway:	n/a
13	chr12:59314400-59314450	HRPEpiC	eye:	n/a
14	chr12:59314400-59314450	HCPEpiC	choroid plexus:	n/a
15	chr12:59314400-59314450	MCF-7	breast:	n/a
16	chr12:59314400-59314450	MCF10A-Er-Src	breast:	n/a
17	chr12:59314400-59314450	HRE	kidney:	n/a
18	chr12:59314400-59314450	AG04449	skin:	fetal
19	chr12:59314400-59314450	GM19239	blood:	n/a
20	chr12:59314400-59314450	NT2-D1	testis:	n/a
21	chr12:59314400-59314450	BE2_C	brain:	n/a
22	chr12:59314400-59314450	GM12891	blood:	n/a
23	chr12:59314400-59314450	PANC-1	pancreas:	n/a
24	chr12:59314400-59314450	IMR90	lung:	fetal
25	chr12:59314400-59314450	AoSMC	blood vessel:	n/a
26	chr12:59314400-59314450	HCF	heart:	n/a
27	chr12:59314400-59314450	U87	brain:	n/a
28	chr12:59314400-59314450	ECC-1	luminal epithelium:	n/a
29	chr12:59314400-59314450	PrEC	prostate:	n/a
30	chr12:59314400-59314450	RPTEC	kidney:	n/a
31	chr12:59314400-59314450	HCT-116	colon:	n/a
32	chr12:59314400-59314450	AG04450	lung:	fetal
33	chr12:59314400-59314450	SK-N-SH_RA	brain:	n/a
34	chr12:59314400-59314450	HMEC	breast:	n/a
35	chr12:59314400-59314450	HEK293	kidney:	embryo
36	chr12:59314400-59314450	LNCaP	prostate:	n/a
37	chr12:59314400-59314450	NH-A	brain:	n/a
38	chr12:59314400-59314450	HEEpiC	esophagus:	n/a
39	chr12:59314400-59314450	Hepatocyte	liver:	n/a
40	chr12:59314400-59314450	Caco-2	colon:	n/a
41	chr12:59314400-59314450	AG09319	gingival:	n/a
42	chr12:59314400-59314450	Jurkat	blood:	n/a
43	chr12:59314400-59314450	T-47D	breast:	n/a
44	chr12:59314400-59314450	HNPCEpiC	eye:	n/a
45	chr12:59314400-59314450	HIPEpiC	eye:	n/a
46	chr12:59314400-59314450	PFSK-1	brain:	n/a
47	chr12:59314400-59314450	Hela-S3	cervix:	n/a
48	chr12:59314400-59314450	HCM	heart:	n/a
49	chr12:59314400-59314450	A549	lung:	n/a
50	chr12:59314400-59314450	ovcar-3	ovarian:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:59306615..59312160-chr12:59312563..59315284,9	MCF-7	breast:
2	chr12:59313255..59314867-chr6:27838598..27840298,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257443	TF binding region
LRIG3	TF binding region
LRIG3	CpG island
ENSG00000257443	CpG island
ENSG00000182572	Chromatin interaction
ENSG00000139263	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10877188	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10877198	0.80[EUR][1000 genomes]
rs11172823	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172824	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172825	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172827	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11172831	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11172833	0.92[EUR][1000 genomes]
rs11172837	0.82[EUR][1000 genomes]
rs11172839	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11172840	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11172846	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11172857	0.82[EUR][1000 genomes]
rs11172858	0.80[EUR][1000 genomes]
rs11172860	0.80[EUR][1000 genomes]
rs11172861	0.80[EUR][1000 genomes]
rs11172862	0.80[EUR][1000 genomes]
rs12368752	0.82[EUR][1000 genomes]
rs12423502	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12424788	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12426212	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12426969	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60522760	0.82[EUR][1000 genomes]
rs60984323	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61754220	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61919461	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61919462	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61919464	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61919465	0.92[EUR][1000 genomes]
rs61919466	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61919469	0.82[EUR][1000 genomes]
rs61919471	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs61919513	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs61919518	0.82[EUR][1000 genomes]
rs61919519	0.82[EUR][1000 genomes]
rs61919520	0.80[EUR][1000 genomes]
rs61919521	0.82[EUR][1000 genomes]
rs61919523	0.82[EUR][1000 genomes]
rs61919524	0.80[EUR][1000 genomes]
rs61919525	0.80[EUR][1000 genomes]
rs6581224	0.80[EUR][1000 genomes]
rs7136193	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7138401	0.82[EUR][1000 genomes]
rs7294684	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7297094	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7301299	0.82[EUR][1000 genomes]
rs7302365	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7303773	0.80[EUR][1000 genomes]
rs7309872	0.82[EUR][1000 genomes]
rs7963207	0.82[EUR][1000 genomes]
rs7968111	0.80[EUR][1000 genomes]
rs7969722	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7970054	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7980136	0.92[EUR][1000 genomes]
rs9645802	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][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	esv2758311	chr12:59022729-59323045	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2759902	chr12:59022729-59323045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59308600-59314600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:59308800-59314600	Active TSS	Stomach Smooth Muscle	stomach
3	chr12:59309000-59314600	Active TSS	HMEC	breast
4	chr12:59309200-59314600	Active TSS	Duodenum Mucosa	Duodenum
5	chr12:59309200-59314600	Active TSS	Fetal Intestine Small	intestine
6	chr12:59309200-59314600	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr12:59309200-59314800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:59309200-59314800	Active TSS	Ovary	ovary
9	chr12:59309200-59315200	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr12:59309400-59315000	Active TSS	Fetal Muscle Trunk	muscle
11	chr12:59309800-59314600	Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr12:59310000-59315000	Active TSS	Fetal Intestine Large	intestine
13	chr12:59310000-59315200	Active TSS	Rectal Smooth Muscle	rectum
14	chr12:59310400-59314800	Active TSS	Psoas Muscle	Psoas
15	chr12:59310400-59315200	Active TSS	Stomach Mucosa	stomach
16	chr12:59310600-59314600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:59310600-59314600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:59310600-59314600	Active TSS	Fetal Stomach	stomach
19	chr12:59310600-59314600	Active TSS	NHLF	lung
20	chr12:59310600-59314800	Active TSS	Right Atrium	heart
21	chr12:59310600-59315000	Active TSS	Fetal Kidney	kidney
22	chr12:59310800-59314600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:59310800-59314600	Active TSS	NHEK	skin
24	chr12:59310800-59314800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:59310800-59314800	Active TSS	Aorta	Aorta
26	chr12:59310800-59315000	Active TSS	Pancreas	Pancrea
27	chr12:59311000-59314600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:59311000-59314600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:59311000-59314600	Active TSS	HSMMtube	muscle
30	chr12:59311000-59314800	Active TSS	Colon Smooth Muscle	Colon
31	chr12:59311000-59314800	Active TSS	Right Ventricle	heart
32	chr12:59311000-59315000	Active TSS	Colonic Mucosa	Colon
33	chr12:59311200-59314600	Active TSS	Brain Hippocampus Middle	brain
34	chr12:59311200-59314600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr12:59311200-59314600	Active TSS	GM12878-XiMat	blood
36	chr12:59311200-59314600	Active TSS	HUVEC	blood vessel
37	chr12:59311200-59314800	Active TSS	HSMM	muscle
38	chr12:59311400-59314600	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr12:59311600-59314600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:59311800-59314800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:59311800-59314800	Bivalent/Poised TSS	Fetal Thymus	thymus
42	chr12:59312000-59314600	Active TSS	Brain Angular Gyrus	brain
43	chr12:59312000-59314600	Active TSS	Brain Cingulate Gyrus	brain
44	chr12:59312000-59314600	Active TSS	NHDF-Ad	bronchial
45	chr12:59312000-59314800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:59312000-59315000	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr12:59312000-59315200	Active TSS	Brain Anterior Caudate	brain
48	chr12:59312200-59314600	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr12:59312200-59314800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:59312200-59314800	Active TSS	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links