Variant report

Variant	rs17010957
Chromosome Location	chr4:86719165-86719166
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:86717537..86719169-chr4:86889518..86891294,13	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10516757	0.93[JPT][hapmap]
rs12498568	0.85[GIH][hapmap]
rs12710823	0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs17010961	1.00[CEU][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17011002	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1823762	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs2014912	0.93[JPT][hapmap];0.84[AMR][1000 genomes]
rs3796625	0.87[CEU][hapmap]
rs6829822	0.84[AMR][1000 genomes]
rs72976750	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72976751	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7671129	0.93[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7687906	0.93[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs7687940	0.93[JPT][hapmap];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461566	chr4:85988032-86725502	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv594747	chr4:85988032-86725502	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv470048	chr4:85998783-86720838	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	esv3450999	chr4:86485840-86773745	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv879517	chr4:86677107-86739805	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17010957	THAP9	cis	parietal	SCAN
rs17010957	SPARCL1	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86701000-86728800	Weak transcription	Right Ventricle	heart
2	chr4:86704000-86719800	Enhancers	NHDF-Ad	bronchial
3	chr4:86705800-86719600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr4:86709000-86727000	Weak transcription	HSMMtube	muscle
5	chr4:86709200-86727000	Weak transcription	HSMM	muscle
6	chr4:86711000-86719800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:86712800-86719400	Weak transcription	Right Atrium	heart
8	chr4:86713200-86726400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr4:86715200-86719800	Weak transcription	Fetal Lung	lung
10	chr4:86716000-86720000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr4:86717800-86719600	Enhancers	Muscle Satellite Cultured Cells	--
12	chr4:86718000-86721800	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr4:86718200-86719200	Weak transcription	Fetal Stomach	stomach
14	chr4:86718200-86719200	Weak transcription	HMEC	breast
15	chr4:86718200-86719600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:86718200-86719800	Enhancers	Liver	Liver
17	chr4:86718200-86728400	Weak transcription	Left Ventricle	heart
18	chr4:86718200-86733800	Weak transcription	Gastric	stomach
19	chr4:86718400-86719600	Enhancers	Adipose Nuclei	Adipose
20	chr4:86718600-86719400	Enhancers	NHLF	lung
21	chr4:86718600-86720400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr4:86718600-86720600	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr4:86718800-86719400	Genic enhancers	Primary B cells from cord blood	blood
24	chr4:86718800-86719400	Weak transcription	A549	lung
25	chr4:86718800-86719800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:86718800-86720000	Enhancers	Osteobl	bone
27	chr4:86718800-86720400	Weak transcription	HUVEC	blood vessel
28	chr4:86719000-86719200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:86719000-86722400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:86719000-86727600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links