Variant report

Variant	rs58869591
Chromosome Location	chr12:50790916-50790917
allele	G/T
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	FOXA2	chr12:50789914-50790976	HepG2	liver:	n/a	chr12:50789997-50790009 chr12:50790581-50790593

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50787607..50792856-chr12:50793045..50797935,10	K562	blood:

Variant related genes	Relation type
LARP4	TF binding region
FAM186A	TF binding region
ENSG00000161813	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10506293	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10747580	0.85[ASN][1000 genomes]
rs10747581	0.85[ASN][1000 genomes]
rs10783362	0.86[ASN][1000 genomes]
rs10783368	0.81[EUR][1000 genomes]
rs10876030	0.88[ASN][1000 genomes]
rs10876034	0.85[ASN][1000 genomes]
rs10876048	0.81[EUR][1000 genomes]
rs10876054	0.81[EUR][1000 genomes]
rs11169408	0.86[ASN][1000 genomes]
rs11169422	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169427	0.85[ASN][1000 genomes]
rs11169440	0.85[ASN][1000 genomes]
rs11503904	0.81[ASN][1000 genomes]
rs12099511	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12099615	0.85[EUR][1000 genomes]
rs12296379	0.85[EUR][1000 genomes]
rs12307602	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12320201	0.81[EUR][1000 genomes]
rs12578525	0.86[ASN][1000 genomes]
rs13328926	0.85[EUR][1000 genomes]
rs1402693	0.85[EUR][1000 genomes]
rs17119774	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17119778	0.87[ASN][1000 genomes]
rs17124672	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17531020	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1996750	0.85[EUR][1000 genomes]
rs28414775	0.85[EUR][1000 genomes]
rs28479152	0.85[EUR][1000 genomes]
rs2947617	0.81[EUR][1000 genomes]
rs4129355	0.81[EUR][1000 genomes]
rs4238104	0.86[ASN][1000 genomes]
rs4257057	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4298982	0.85[ASN][1000 genomes]
rs4306347	0.85[EUR][1000 genomes]
rs4351895	0.86[ASN][1000 genomes]
rs4450234	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4517607	0.85[EUR][1000 genomes]
rs4768877	0.83[ASN][1000 genomes]
rs4768878	0.85[ASN][1000 genomes]
rs4768879	0.86[ASN][1000 genomes]
rs4768880	0.85[ASN][1000 genomes]
rs4768887	0.81[EUR][1000 genomes]
rs4768928	0.91[ASN][1000 genomes]
rs4768936	0.88[ASN][1000 genomes]
rs56671180	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56753963	0.85[EUR][1000 genomes]
rs56989201	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57283487	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57293958	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57512759	0.85[EUR][1000 genomes]
rs57578212	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57811009	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57828015	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58500867	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58888905	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58915267	0.89[EUR][1000 genomes]
rs58916974	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59163743	0.83[AMR][1000 genomes]
rs59194948	0.85[EUR][1000 genomes]
rs59683461	0.85[EUR][1000 genomes]
rs59696942	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59968707	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60010359	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60198651	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60201334	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60239257	0.85[EUR][1000 genomes]
rs60242613	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60396677	0.95[EUR][1000 genomes]
rs60420087	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60494920	0.85[EUR][1000 genomes]
rs60610745	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60743903	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61578731	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6580753	0.86[ASN][1000 genomes]
rs6580754	0.85[ASN][1000 genomes]
rs7131993	0.81[EUR][1000 genomes]
rs7133488	0.87[ASN][1000 genomes]
rs7135159	0.83[ASN][1000 genomes]
rs7135222	0.81[EUR][1000 genomes]
rs7138063	0.85[ASN][1000 genomes]
rs7295610	0.87[ASN][1000 genomes]
rs7296212	0.89[ASN][1000 genomes]
rs7299321	0.87[ASN][1000 genomes]
rs7301125	0.81[EUR][1000 genomes]
rs7302749	0.81[EUR][1000 genomes]
rs7304017	0.84[ASN][1000 genomes]
rs7304262	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7306387	0.85[EUR][1000 genomes]
rs74090120	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7487645	0.85[EUR][1000 genomes]
rs7953880	0.85[EUR][1000 genomes]
rs7955176	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7955310	0.81[EUR][1000 genomes]
rs7957033	0.86[ASN][1000 genomes]
rs7965165	0.85[ASN][1000 genomes]
rs7974480	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7978443	0.85[EUR][1000 genomes]
rs7978625	0.87[ASN][1000 genomes]
rs9634264	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers 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	56 gene(s)	inside rSNPs	diseases
2	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv1053667	chr12:50679039-50801752	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1054480	chr12:50691039-50859665	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv1041563	chr12:50705715-50861699	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv1049665	chr12:50705715-50871542	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS 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	30 gene(s)	inside rSNPs	diseases
7	nsv899076	chr12:50770291-50869589	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50781800-50794000	Weak transcription	Fetal Kidney	kidney
2	chr12:50782000-50794000	Weak transcription	Fetal Heart	heart
3	chr12:50782800-50794200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:50785000-50794000	Weak transcription	HUVEC	blood vessel
5	chr12:50788000-50791000	Enhancers	NHDF-Ad	bronchial
6	chr12:50788000-50791400	Enhancers	HepG2	liver
7	chr12:50789600-50791000	Enhancers	Osteobl	bone
8	chr12:50789600-50791200	Enhancers	Hela-S3	cervix
9	chr12:50789800-50791400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:50790000-50791400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:50790200-50794000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:50790400-50791200	Enhancers	HMEC	breast
13	chr12:50790400-50793800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:50790600-50791000	Enhancers	A549	lung
15	chr12:50790600-50791400	Enhancers	Placenta	Placenta
16	chr12:50790600-50793600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:50790600-50793800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:50790600-50794000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:50790600-50794200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr12:50790800-50793800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:50790800-50793800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr12:50790800-50793800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:50790800-50793800	Weak transcription	NHEK	skin
24	chr12:50790800-50794000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:50790800-50794000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:50790800-50794200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links