Variant report

Variant	rs11133257
Chromosome Location	chr4:54120462-54120463
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10007422	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11133251	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11133252	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11724062	0.83[CEU][hapmap]
rs11731676	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11933772	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11945292	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12507517	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.83[ASN][1000 genomes]
rs12509702	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13103971	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13113985	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13130986	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13152012	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1383981	0.83[CEU][hapmap]
rs1383983	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1481817	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1481818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1481821	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17705869	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1842658	0.83[CEU][hapmap]
rs1871826	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2054588	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2412397	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412400	0.89[ASN][1000 genomes]
rs2412402	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28765170	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28795373	0.80[ASN][1000 genomes]
rs34115081	0.83[ASN][1000 genomes]
rs3986366	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4103016	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4254834	0.95[ASN][1000 genomes]
rs4385132	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4435800	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4472196	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4515222	0.86[ASN][1000 genomes]
rs4864743	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4864748	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4864749	0.83[CEU][hapmap]
rs56056061	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62324288	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62324326	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6554068	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6554072	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.94[YRI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6554077	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6554089	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6554091	0.83[CEU][hapmap]
rs6810608	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6818181	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6828377	0.87[ASN][1000 genomes]
rs6830743	0.83[ASN][1000 genomes]
rs6839876	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6840571	0.83[ASN][1000 genomes]
rs6846461	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71597825	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7441849	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7654397	0.83[ASN][1000 genomes]
rs7657388	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7682970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7683984	0.83[CEU][hapmap]
rs7698145	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7699124	0.83[AMR][1000 genomes]
rs900110	0.83[CEU][hapmap]
rs900111	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs922748	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9684264	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9761504	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9990771	0.83[CEU][hapmap]
rs9998307	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9998376	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997614	chr4:54086727-54150632	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv879013	chr4:54093717-54137228	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1008593	chr4:54120297-54207769	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 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	chr4:54101600-54129400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:54108400-54129600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr4:54114400-54134400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:54114400-54139600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:54114400-54144000	Weak transcription	Liver	Liver
6	chr4:54114600-54121000	Weak transcription	Pancreas	Pancrea
7	chr4:54114600-54126400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:54114600-54129800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:54114800-54129400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:54114800-54130000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr4:54117800-54132800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:54119600-54130400	Weak transcription	NHLF	lung
13	chr4:54120200-54120600	ZNF genes & repeats	Fetal Lung	lung
14	chr4:54120400-54120600	ZNF genes & repeats	Primary T cells from cord blood	blood
15	chr4:54120400-54120600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:54120400-54120600	ZNF genes & repeats	Fetal Stomach	stomach

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