Variant report

Variant	rs4584419
Chromosome Location	chr1:57109660-57109661
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	FOXA2	chr1:57109189-57110009	HepG2	liver:	n/a	n/a
2	FOXA1	chr1:57109241-57109708	HepG2	liver:	n/a	n/a
3	FOXA1	chr1:57109311-57109713	HepG2	liver:	n/a	n/a
4	ARID3A	chr1:57109126-57110185	HepG2	liver:	n/a	n/a
5	EP300	chr1:57109310-57109682	HepG2	liver:	n/a	n/a
6	GATA2	chr1:57109506-57110121	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
PRKAA2	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10749708	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10789036	1.00[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789038	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10789040	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10789041	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10889006	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10889008	1.00[ASW][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10889009	0.85[ASN][1000 genomes]
rs11206884	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11206885	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11206886	0.91[ASN][1000 genomes]
rs11206888	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11206889	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11206890	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11206895	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1124900	0.81[AMR][1000 genomes]
rs11589368	0.85[ASN][1000 genomes]
rs11804779	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12021768	0.95[ASN][1000 genomes]
rs12021851	0.95[ASN][1000 genomes]
rs12023668	0.85[ASN][1000 genomes]
rs12032999	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12046428	0.83[ASN][1000 genomes]
rs12048572	0.85[ASN][1000 genomes]
rs12073311	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12078260	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.98[LWK][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12092267	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12097148	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12738355	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13374924	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1418442	0.92[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.85[ASN][1000 genomes]
rs1986660	0.95[ASN][1000 genomes]
rs2404718	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2404992	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2404993	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2746345	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2746348	1.00[ASW][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.87[TSI][hapmap]
rs2746349	1.00[ASW][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap]
rs2746353	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2796517	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2796519	1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2796523	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2796527	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4548471	0.95[ASN][1000 genomes]
rs4551620	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4562656	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59223968	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61772962	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61774287	0.95[ASN][1000 genomes]
rs61774288	0.90[AFR][1000 genomes]
rs6588641	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72666470	0.90[ASN][1000 genomes]
rs7419053	0.92[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.85[ASN][1000 genomes]
rs7515414	0.92[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.83[ASN][1000 genomes]
rs7519509	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545066	0.83[ASN][1000 genomes]
rs7546264	0.85[ASN][1000 genomes]
rs7547486	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs932447	0.92[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.85[ASN][1000 genomes]
rs9887834	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9887940	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3371942	chr1:57109389-57112237	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57105600-57110000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:57105600-57110200	Weak transcription	HSMMtube	muscle
3	chr1:57105800-57109800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:57108400-57109800	Enhancers	Hela-S3	cervix
5	chr1:57109000-57109800	Enhancers	Fetal Heart	heart
6	chr1:57109000-57109800	Enhancers	HepG2	liver
7	chr1:57109200-57109800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:57109200-57109800	Bivalent Enhancer	Fetal Kidney	kidney
9	chr1:57109200-57110000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:57109200-57110000	Enhancers	Fetal Intestine Small	intestine
11	chr1:57109400-57109800	Enhancers	HUVEC	blood vessel
12	chr1:57109400-57110000	Enhancers	Liver	Liver
13	chr1:57109400-57110000	Enhancers	NHDF-Ad	bronchial
14	chr1:57109600-57109800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
15	chr1:57109600-57109800	Enhancers	Fetal Intestine Large	intestine
16	chr1:57109600-57109800	Enhancers	Fetal Stomach	stomach
17	chr1:57109600-57109800	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr1:57109600-57109800	Enhancers	A549	lung
19	chr1:57109600-57110200	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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