Variant report

Variant	rs61919461
Chromosome Location	chr12:59315540-59315541
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr12:59315176-59315666	HepG2	liver:	n/a	n/a
2	MYBL2	chr12:59315272-59315688	HepG2	liver:	n/a	n/a
3	HNF4G	chr12:59315337-59315616	HepG2	liver:	n/a	n/a
4	HDAC2	chr12:59315282-59315593	HepG2	liver:	n/a	n/a
5	HNF4A	chr12:59315356-59315627	HepG2	liver:	n/a	n/a
6	RXRA	chr12:59315300-59315560	HepG2	liver:	n/a	chr12:59315372-59315381
7	SP1	chr12:59315299-59315635	HepG2	liver:	n/a	n/a
8	CEBPB	chr12:59315065-59315613	HepG2	liver:	n/a	n/a
9	SMC3	chr12:59315290-59315582	HepG2	liver:	n/a	n/a
10	EP300	chr12:59315270-59315611	HepG2	liver:	n/a	n/a
11	ARID3A	chr12:59315348-59315686	HepG2	liver:	n/a	n/a
12	EP300	chr12:59315206-59315606	HepG2	liver:	n/a	n/a
13	MYBL2	chr12:59315210-59315736	HepG2	liver:	n/a	n/a
14	CEBPB	chr12:59315308-59315614	H1-hESC	embryonic stem cell:	n/a	n/a
15	HNF4A	chr12:59315345-59315658	HepG2	liver:	n/a	n/a
16	CEBPB	chr12:59315239-59315612	HepG2	liver:	n/a	n/a
17	HNF4G	chr12:59315165-59315639	HepG2	liver:	n/a	n/a
18	FOXA2	chr12:59315330-59315559	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:59308294..59310452-chr12:59314472..59316153,2	K562	blood:

No data

Variant related genes	Relation type
LRIG3	TF binding region
ENSG00000139263	Chromatin interaction

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

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

rs_ID	r²[population]
rs10877188	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10877198	0.85[EUR][1000 genomes]
rs10877200	0.81[EUR][1000 genomes]
rs11172823	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11172824	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11172825	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11172827	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11172831	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11172833	0.97[EUR][1000 genomes]
rs11172837	0.87[EUR][1000 genomes]
rs11172839	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11172840	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11172846	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11172857	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11172858	0.85[EUR][1000 genomes]
rs11172860	0.85[EUR][1000 genomes]
rs11172861	0.85[EUR][1000 genomes]
rs11172862	0.85[EUR][1000 genomes]
rs11172866	0.81[EUR][1000 genomes]
rs11172867	0.81[EUR][1000 genomes]
rs11172868	0.83[EUR][1000 genomes]
rs12368752	0.87[EUR][1000 genomes]
rs12370522	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12423502	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12424788	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12426212	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12426969	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17121828	0.81[EUR][1000 genomes]
rs55888651	0.81[EUR][1000 genomes]
rs58692617	0.84[EUR][1000 genomes]
rs60522760	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60984323	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61754220	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61919462	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61919464	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61919465	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61919466	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61919469	0.87[EUR][1000 genomes]
rs61919471	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61919513	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61919518	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61919519	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61919520	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61919521	0.87[EUR][1000 genomes]
rs61919523	0.87[EUR][1000 genomes]
rs61919524	0.85[EUR][1000 genomes]
rs61919525	0.85[EUR][1000 genomes]
rs61919531	0.84[EUR][1000 genomes]
rs61919532	0.84[EUR][1000 genomes]
rs6581224	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7136193	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7138401	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7294684	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7297094	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7301299	0.87[EUR][1000 genomes]
rs7302365	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7303773	0.85[EUR][1000 genomes]
rs7309872	0.87[EUR][1000 genomes]
rs7963207	0.87[EUR][1000 genomes]
rs7968111	0.85[EUR][1000 genomes]
rs7969722	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7970054	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7980136	0.97[EUR][1000 genomes]
rs7980483	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9645802	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[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:43 , 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	chr12:59314400-59316400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:59314400-59318200	Weak transcription	Small Intestine	intestine
4	chr12:59314600-59317200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:59314800-59315600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:59314800-59315600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr12:59314800-59315600	Enhancers	HMEC	breast
8	chr12:59314800-59315800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr12:59314800-59319000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:59315000-59315600	Enhancers	Liver	Liver
11	chr12:59315000-59315600	Enhancers	HUVEC	blood vessel
12	chr12:59315000-59315600	Enhancers	NHEK	skin
13	chr12:59315000-59316600	Weak transcription	NH-A	brain
14	chr12:59315000-59316600	Weak transcription	NHDF-Ad	bronchial
15	chr12:59315000-59318400	Weak transcription	Fetal Heart	heart
16	chr12:59315000-59318800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr12:59315000-59318800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr12:59315000-59319200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr12:59315200-59315600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:59315200-59315600	Enhancers	Pancreas	Pancrea
21	chr12:59315200-59316200	Weak transcription	Hela-S3	cervix
22	chr12:59315200-59316400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:59315200-59316400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:59315200-59316400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:59315200-59316400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:59315200-59316600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:59315200-59316600	Weak transcription	A549	lung
28	chr12:59315200-59316600	Weak transcription	Osteobl	bone
29	chr12:59315200-59317000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:59315200-59320200	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr12:59315400-59315800	Weak transcription	Colonic Mucosa	Colon
32	chr12:59315400-59316600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:59315400-59316600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:59315400-59316600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr12:59315400-59316600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:59315400-59316600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr12:59315400-59316600	Weak transcription	Stomach Mucosa	stomach
38	chr12:59315400-59316800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr12:59315400-59316800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr12:59315400-59318600	Weak transcription	Fetal Lung	lung
41	chr12:59315400-59320200	Enhancers	Fetal Intestine Large	intestine
42	chr12:59315400-59320800	Enhancers	Fetal Intestine Small	intestine
43	chr12:59315400-59320800	Weak transcription	Fetal Muscle Leg	muscle

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