Variant report

Variant	rs4584622
Chromosome Location	chr12:72672823-72672824
allele	C/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	FOXA1	chr12:72672766-72672991	T-47D	breast:	n/a	chr12:72672936-72672951 chr12:72672891-72672903
2	GATA3	chr12:72672689-72673003	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:72666745..72669192-chr12:72671780..72674758,2	K562	blood:
2	chr12:72672668..72675392-chr12:72676905..72679319,3	K562	blood:

Variant related genes	Relation type
TRHDE-AS1	TF binding region
ENSG00000072657	Chromatin interaction
ENSG00000236333	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10506650	0.96[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs10506652	0.96[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs10784960	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10879387	0.90[EUR][1000 genomes]
rs10879391	0.95[EUR][1000 genomes]
rs10879392	0.96[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs10879394	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10879398	0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs11179146	0.97[EUR][1000 genomes]
rs11609294	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12229324	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.98[EUR][1000 genomes]
rs17110954	0.85[JPT][hapmap]
rs3803030	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs4073007	0.85[JPT][hapmap]
rs4237861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4254109	0.88[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs4262761	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs4360737	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4423229	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4587772	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4639975	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760827	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760829	0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs6421234	0.83[CEU][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes]
rs7135786	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs7295741	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307765	0.88[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes]
rs7963246	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7974998	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422452	chr12:72485933-73175581	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv899257	chr12:72569746-73145896	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv832452	chr12:72584971-72764495	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv899258	chr12:72624088-72957899	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv559362	chr12:72641784-72694691	Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv1044083	chr12:72647640-73275526	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv469465	chr12:72655925-73259114	Weak transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv559363	chr12:72655925-73259114	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv868884	chr12:72664763-73241518	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:72669000-72673400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:72670600-72673400	Weak transcription	HMEC	breast
3	chr12:72670600-72674200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:72670600-72674200	Weak transcription	Ovary	ovary
5	chr12:72671000-72674600	Enhancers	Fetal Intestine Small	intestine
6	chr12:72671000-72674800	Enhancers	Fetal Intestine Large	intestine
7	chr12:72671400-72673400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:72671800-72674200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr12:72672000-72674000	Weak transcription	NH-A	brain
10	chr12:72672200-72673000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:72672200-72681800	Weak transcription	Adipose Nuclei	Adipose
12	chr12:72672200-72685000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:72672800-72673000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:72672800-72673200	Enhancers	Fetal Kidney	kidney
15	chr12:72672800-72674600	Enhancers	Pancreas	Pancrea
16	chr12:72672800-72676800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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