Variant report

Variant	rs6599282
Chromosome Location	chr4:1108407-1108408
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:1108188..1111933-chr4:1241185..1244027,3	MCF-7	breast:
2	chr4:1106466..1109450-chr4:1112409..1114063,2	K562	blood:

Variant related genes	Relation type
ENSG00000212458	Chromatin interaction
ENSG00000196810	Chromatin interaction
ENSG00000159692	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10002248	1.00[CEU][hapmap];0.84[MKK][hapmap]
rs10002437	1.00[CEU][hapmap];0.84[MKK][hapmap]
rs10003030	0.87[ASW][hapmap];0.84[LWK][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs10014245	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs10015944	0.97[AFR][1000 genomes]
rs10016588	0.93[YRI][hapmap];0.91[AFR][1000 genomes]
rs10032349	0.80[EUR][1000 genomes]
rs10032470	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs10033163	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs11724989	0.88[CEU][hapmap]
rs11726554	0.94[AFR][1000 genomes]
rs11728360	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11731643	0.85[AFR][1000 genomes]
rs11731685	0.95[AFR][1000 genomes]
rs11736950	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13119696	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1383660	0.88[CEU][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs1481167	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17164384	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs28540372	0.81[AFR][1000 genomes]
rs28621675	0.98[AFR][1000 genomes]
rs28785628	0.98[AFR][1000 genomes]
rs28856334	0.88[AFR][1000 genomes]
rs2924495	0.88[CEU][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs3775111	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs4246683	0.83[EUR][1000 genomes]
rs4246684	0.88[CEU][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs4974561	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs4974569	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs4974571	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs4974573	0.88[CEU][hapmap]
rs4974628	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs4974637	0.80[EUR][1000 genomes]
rs4974639	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs4974642	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs4974643	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs4974644	0.88[CEU][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs588824	0.88[CEU][hapmap]
rs589660	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs59465697	0.95[AFR][1000 genomes]
rs604526	0.85[CEU][hapmap]
rs606327	0.88[CEU][hapmap]
rs608066	0.86[CEU][hapmap]
rs614945	0.88[CEU][hapmap]
rs615381	0.88[CEU][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs616569	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs619407	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs620398	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs629638	0.88[CEU][hapmap]
rs632319	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs633087	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs633141	0.88[CEU][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs633599	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs633954	0.88[CEU][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs643043	1.00[CEU][hapmap]
rs646117	0.80[EUR][1000 genomes]
rs647828	0.80[EUR][1000 genomes]
rs648640	0.80[EUR][1000 genomes]
rs649243	0.88[CEU][hapmap]
rs649258	0.80[EUR][1000 genomes]
rs649616	0.88[CEU][hapmap];0.92[GIH][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs6599283	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6599284	1.00[CEU][hapmap];0.86[MKK][hapmap]
rs6599285	1.00[CEU][hapmap]
rs661364	0.80[EUR][1000 genomes]
rs671790	0.88[CEU][hapmap]
rs6812059	0.82[AFR][1000 genomes]
rs6814094	0.80[EUR][1000 genomes]
rs6817989	0.88[CEU][hapmap];0.92[GIH][hapmap]
rs681857	0.88[CEU][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs682243	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs682787	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs6831018	0.90[AFR][1000 genomes]
rs6836158	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs6836335	1.00[CEU][hapmap]
rs6839768	0.88[CEU][hapmap];1.00[GIH][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs6840162	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs6840347	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs73067706	0.86[AFR][1000 genomes]
rs73067775	0.94[AFR][1000 genomes]
rs73067776	0.94[AFR][1000 genomes]
rs73072227	0.80[AMR][1000 genomes]
rs7661069	0.81[ASW][hapmap];0.82[LWK][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs7669287	0.87[ASW][hapmap];0.84[LWK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs7676956	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7679718	1.00[CEU][hapmap];0.86[MKK][hapmap]
rs7684536	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7685051	0.98[AFR][1000 genomes]
rs7690300	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7690832	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs878324	0.85[AFR][1000 genomes]
rs9992322	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv536980	chr4:827866-1167377	Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv1009619	chr4:901897-1215657	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv1003876	chr4:927509-1191316	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1000381	chr4:927509-1198766	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	esv3339080	chr4:970630-1546223	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
8	nsv1004727	chr4:1015652-1158207	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv536984	chr4:1015652-1158207	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv1005990	chr4:1015652-1167619	Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv1000594	chr4:1045099-1129975	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv1001165	chr4:1051512-1129975	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv1012892	chr4:1086871-1176630	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv829835	chr4:1097586-1304239	Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
15	esv3440980	chr4:1105477-1108525	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	esv3374334	chr4:1105777-1108900	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	esv3375020	chr4:1106377-1109125	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 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	chr4:1104600-1109600	Weak transcription	Fetal Kidney	kidney
2	chr4:1107000-1108600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
3	chr4:1107400-1108600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:1107600-1108600	Weak transcription	Esophagus	oesophagus
5	chr4:1107600-1108800	Enhancers	Colonic Mucosa	Colon
6	chr4:1107800-1109200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:1108200-1108600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr4:1108200-1108600	Enhancers	Adipose Nuclei	Adipose
9	chr4:1108200-1108600	Weak transcription	Pancreas	Pancrea
10	chr4:1108200-1109000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:1108200-1109600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:1108400-1108600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr4:1108400-1108600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:1108400-1108600	Flanking Active TSS	Hela-S3	cervix
15	chr4:1108400-1108600	Enhancers	Osteobl	bone
16	chr4:1108400-1108800	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links