Variant report

Variant	rs10016588
Chromosome Location	chr4:1109855-1109856
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:1108188..1111933-chr4:1241185..1244027,3	MCF-7	breast:
2	chr4:1065925..1067549-chr4:1109315..1111845,2	MCF-7	breast:
3	chr4:1109287..1111564-chr4:1115263..1117535,2	K562	blood:
4	chr4:1109287..1111934-chr4:1115263..1117139,2	K562	blood:

Variant related genes	Relation type
ENSG00000215367	Chromatin interaction
ENSG00000196810	Chromatin interaction
ENSG00000178222	Chromatin interaction
ENSG00000159692	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10003030	0.93[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10014245	0.93[YRI][hapmap];0.87[AFR][1000 genomes]
rs10015944	0.89[AFR][1000 genomes]
rs11723211	0.98[ASN][1000 genomes]
rs11726554	0.85[AFR][1000 genomes]
rs11726675	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11726836	0.98[ASN][1000 genomes]
rs11731643	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11731685	0.87[AFR][1000 genomes]
rs11735226	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1481167	0.90[YRI][hapmap];0.91[AFR][1000 genomes]
rs17164362	0.95[ASN][1000 genomes]
rs17164373	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17164382	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17164384	0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs2001862	0.95[ASN][1000 genomes]
rs28540372	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs28621675	0.89[AFR][1000 genomes]
rs28785628	0.89[AFR][1000 genomes]
rs3775110	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3775111	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59465697	0.87[AFR][1000 genomes]
rs6599282	0.93[YRI][hapmap];0.91[AFR][1000 genomes]
rs6599283	0.93[YRI][hapmap];0.91[AFR][1000 genomes]
rs6831018	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6836158	0.93[YRI][hapmap];0.91[AFR][1000 genomes]
rs6853712	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73067775	0.85[AFR][1000 genomes]
rs73067776	0.85[AFR][1000 genomes]
rs7659054	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7661069	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7669287	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7676956	0.93[YRI][hapmap];0.91[AFR][1000 genomes]
rs7684536	0.93[YRI][hapmap];0.91[AFR][1000 genomes]
rs7685051	0.90[AFR][1000 genomes]
rs7690300	0.90[YRI][hapmap];0.91[AFR][1000 genomes]
rs7690832	0.93[YRI][hapmap];0.87[AFR][1000 genomes]
rs878324	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1108800-1110200	Enhancers	Hela-S3	cervix
2	chr4:1108800-1115800	Weak transcription	Pancreas	Pancrea
3	chr4:1109400-1110200	Enhancers	Liver	Liver
4	chr4:1109600-1110800	Enhancers	Fetal Kidney	kidney
5	chr4:1109600-1110800	Enhancers	HepG2	liver
6	chr4:1109800-1110200	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr4:1109800-1110800	Weak transcription	Duodenum Mucosa	Duodenum

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