Variant report

Variant	rs7294684
Chromosome Location	chr12:59316674-59316675
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	SMC3	chr12:59316641-59317259	Hela-S3	cervix:	n/a	n/a
2	TCF12	chr12:59316497-59317145	A549	lung:	n/a	n/a
3	RCOR1	chr12:59316667-59317137	Hela-S3	cervix:	n/a	n/a
4	RAD21	chr12:59316631-59317121	Hela-S3	cervix:	n/a	n/a
5	USF2	chr12:59316669-59316980	Hela-S3	cervix:	n/a	n/a
6	GATA2	chr12:59316588-59317479	HUVEC	blood vessel:	n/a	chr12:59317321-59317328 chr12:59317321-59317328 chr12:59317321-59317328
7	CHD2	chr12:59316552-59317034	Hela-S3	cervix:	n/a	n/a
8	CEBPB	chr12:59316535-59317160	Hela-S3	cervix:	n/a	n/a
9	FOS	chr12:59316661-59317019	MCF10A-Er-Src	breast:	n/a	n/a
10	EP300	chr12:59316631-59317116	Hela-S3	cervix:	n/a	n/a
11	TFAP2C	chr12:59316578-59317017	Hela-S3	cervix:	n/a	chr12:59316747-59316762

Variant related genes	Relation type
LRIG3	TF binding region

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

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10877188	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877198	0.88[EUR][1000 genomes]
rs10877200	0.83[EUR][1000 genomes]
rs11172823	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11172824	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11172825	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11172827	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172831	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11172833	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11172837	0.89[EUR][1000 genomes]
rs11172839	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11172840	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11172846	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11172857	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11172858	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11172860	0.88[EUR][1000 genomes]
rs11172861	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11172862	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11172866	0.83[EUR][1000 genomes]
rs11172867	0.83[EUR][1000 genomes]
rs11172868	0.85[EUR][1000 genomes]
rs12368752	0.89[EUR][1000 genomes]
rs12370522	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12423502	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12424788	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12426212	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12426969	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17121828	0.83[EUR][1000 genomes]
rs55888651	0.83[EUR][1000 genomes]
rs58692617	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60522760	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60984323	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61754220	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61919461	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61919462	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61919464	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61919465	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61919466	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61919469	0.89[EUR][1000 genomes]
rs61919471	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61919513	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61919518	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61919519	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61919520	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61919521	0.89[EUR][1000 genomes]
rs61919523	0.89[EUR][1000 genomes]
rs61919524	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61919525	0.88[EUR][1000 genomes]
rs61919531	0.87[EUR][1000 genomes]
rs61919532	0.87[EUR][1000 genomes]
rs6581224	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7136193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138401	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7297094	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7301299	0.89[EUR][1000 genomes]
rs7302365	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7303773	0.88[EUR][1000 genomes]
rs7309872	0.89[EUR][1000 genomes]
rs7963207	0.89[EUR][1000 genomes]
rs7968111	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7969722	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7970054	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7980136	1.00[EUR][1000 genomes]
rs7980483	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9645802	0.83[AFR][1000 genomes];0.96[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	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:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59313400-59317200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:59314400-59318200	Weak transcription	Small Intestine	intestine
3	chr12:59314600-59317200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:59314800-59319000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:59315000-59318400	Weak transcription	Fetal Heart	heart
6	chr12:59315000-59318800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:59315000-59318800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr12:59315000-59319200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr12:59315200-59317000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:59315200-59320200	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr12:59315400-59316800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:59315400-59316800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:59315400-59318600	Weak transcription	Fetal Lung	lung
14	chr12:59315400-59320200	Enhancers	Fetal Intestine Large	intestine
15	chr12:59315400-59320800	Enhancers	Fetal Intestine Small	intestine
16	chr12:59315400-59320800	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:59315600-59318800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:59315600-59318800	Weak transcription	Liver	Liver
19	chr12:59315600-59318800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr12:59316000-59318800	Enhancers	HUVEC	blood vessel
21	chr12:59316000-59319600	Weak transcription	Colonic Mucosa	Colon
22	chr12:59316200-59319800	Enhancers	Hela-S3	cervix
23	chr12:59316400-59316800	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr12:59316400-59316800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:59316400-59317200	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr12:59316400-59317400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:59316400-59317600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr12:59316600-59317000	Enhancers	A549	lung
29	chr12:59316600-59317000	Enhancers	Osteobl	bone
30	chr12:59316600-59317200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:59316600-59317200	Enhancers	Muscle Satellite Cultured Cells	--
32	chr12:59316600-59317200	Enhancers	Pancreas	Pancrea
33	chr12:59316600-59317200	Enhancers	NH-A	brain
34	chr12:59316600-59317200	Enhancers	NHDF-Ad	bronchial
35	chr12:59316600-59317400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:59316600-59317400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:59316600-59317400	Enhancers	Stomach Mucosa	stomach
38	chr12:59316600-59318000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:59316600-59318000	Enhancers	Duodenum Mucosa	Duodenum
40	chr12:59316600-59318200	Enhancers	HMEC	breast
41	chr12:59316600-59318400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:59316600-59319400	Enhancers	NHEK	skin

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