Variant report

Variant	rs10509556
Chromosome Location	chr10:90599996-90599997
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	chr10:90599319..90601374-chr10:90601380..90603688,2	MCF-7	breast:
2	chr10:90599583..90601963-chr10:90608850..90611215,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1029024	1.00[CHB][hapmap]
rs10509555	0.89[CHB][hapmap];1.00[EUR][1000 genomes]
rs10509558	0.82[CHB][hapmap];1.00[EUR][1000 genomes]
rs10509559	0.83[CHB][hapmap];1.00[EUR][1000 genomes]
rs11202885	1.00[EUR][1000 genomes]
rs12242274	0.82[CHB][hapmap];1.00[EUR][1000 genomes]
rs12243282	0.83[CHB][hapmap];1.00[EUR][1000 genomes]
rs12243621	0.83[CHB][hapmap];1.00[EUR][1000 genomes]
rs12245525	1.00[EUR][1000 genomes]
rs12245668	1.00[EUR][1000 genomes]
rs12254451	1.00[EUR][1000 genomes]
rs12257540	0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs12260572	0.83[CHB][hapmap];1.00[EUR][1000 genomes]
rs12262461	0.83[CHB][hapmap]
rs12263461	1.00[EUR][1000 genomes]
rs12413277	0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs12414800	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs17113311	0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs17113344	0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs17113363	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs17113426	0.92[CHB][hapmap];1.00[EUR][1000 genomes]
rs17113457	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17113476	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17113724	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17113942	0.83[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17113959	0.83[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17114000	0.82[CHB][hapmap];1.00[EUR][1000 genomes]
rs17114016	0.83[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17114020	0.83[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17114024	0.83[CHB][hapmap];1.00[EUR][1000 genomes]
rs17114057	0.83[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2231780	0.83[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2231785	0.83[CHB][hapmap];1.00[EUR][1000 genomes]
rs2231786	0.82[CHB][hapmap];1.00[EUR][1000 genomes]
rs2282122	0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs35996190	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3814691	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs3898173	0.83[CHB][hapmap];1.00[EUR][1000 genomes]
rs3898174	0.83[CHB][hapmap];1.00[EUR][1000 genomes]
rs56998609	1.00[EUR][1000 genomes]
rs58673564	1.00[EUR][1000 genomes]
rs58986570	1.00[EUR][1000 genomes]
rs59661152	1.00[EUR][1000 genomes]
rs60349051	1.00[EUR][1000 genomes]
rs60523093	1.00[EUR][1000 genomes]
rs7077019	1.00[EUR][1000 genomes]
rs7090604	1.00[EUR][1000 genomes]
rs7098246	1.00[EUR][1000 genomes]
rs72474859	1.00[ASN][1000 genomes]
rs73364839	1.00[EUR][1000 genomes]
rs73364841	1.00[EUR][1000 genomes]
rs73364851	1.00[EUR][1000 genomes]
rs7913997	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer 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 miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv467415	chr10:90478483-90600865	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv551840	chr10:90478483-90600865	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	nsv831942	chr10:90564697-90730352	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 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	chr10:90578000-90607200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr10:90578600-90611200	Weak transcription	Esophagus	oesophagus
3	chr10:90589000-90608800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr10:90593800-90600800	Weak transcription	Fetal Thymus	thymus
5	chr10:90595600-90600800	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr10:90596600-90600200	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr10:90596800-90600200	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr10:90597000-90601000	Weak transcription	GM12878-XiMat	blood
9	chr10:90597600-90601800	Enhancers	Stomach Mucosa	stomach
10	chr10:90598200-90601000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr10:90598800-90601800	Enhancers	Fetal Intestine Large	intestine
12	chr10:90598800-90608000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr10:90599000-90601600	Enhancers	Fetal Intestine Small	intestine
14	chr10:90599600-90600000	Flanking Active TSS	Liver	Liver
15	chr10:90599600-90600400	Flanking Active TSS	A549	lung
16	chr10:90599600-90600600	Weak transcription	Pancreas	Pancrea
17	chr10:90599600-90601200	Enhancers	Duodenum Mucosa	Duodenum
18	chr10:90599600-90605000	Weak transcription	Gastric	stomach
19	chr10:90599800-90601400	Enhancers	NHEK	skin

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