Variant report

Variant	rs17015052
Chromosome Location	chr4:90051503-90051504
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	chr4:90030188..90033002-chr4:90049823..90052502,2	MCF-7	breast:
2	chr4:90043393..90046238-chr4:90047056..90051826,4	K562	blood:

Variant related genes	Relation type
ENSG00000271359	Chromatin interaction
ENSG00000138640	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10033484	0.95[JPT][hapmap]
rs11737182	0.95[JPT][hapmap]
rs12640018	0.82[ASN][1000 genomes]
rs13138280	0.91[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs1398940	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1398944	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1458557	0.95[JPT][hapmap]
rs16996143	0.96[JPT][hapmap]
rs17015027	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1708668	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1708669	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1708670	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs1795722	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1795727	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs1795734	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1795738	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1903007	0.95[JPT][hapmap]
rs1921679	0.91[JPT][hapmap]
rs1921684	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1961979	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2018779	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2085601	0.95[JPT][hapmap]
rs2090031	0.82[ASN][1000 genomes]
rs2178583	0.95[JPT][hapmap]
rs2178584	0.95[JPT][hapmap]
rs2178585	0.95[JPT][hapmap]
rs2609275	0.95[JPT][hapmap]
rs2670623	0.84[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2704571	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2704573	0.96[JPT][hapmap]
rs2704577	0.95[JPT][hapmap]
rs28628620	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869971	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2869972	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2904261	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs35624987	0.83[AFR][1000 genomes]
rs3927227	0.83[ASN][1000 genomes]
rs4285052	0.84[ASN][1000 genomes]
rs4491985	0.87[ASN][1000 genomes]
rs4507326	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs4642211	0.91[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes]
rs59924504	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60618725	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62306363	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62306364	0.84[ASN][1000 genomes]
rs62306390	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62306391	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62306397	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62306424	0.87[ASN][1000 genomes]
rs6821678	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6844655	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs6852373	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6853480	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72877642	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs756345	0.87[ASN][1000 genomes]
rs7656238	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs7658455	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7686954	0.95[JPT][hapmap]
rs7692291	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7697075	0.95[JPT][hapmap]
rs7697900	0.95[JPT][hapmap]
rs9307054	0.95[JPT][hapmap]
rs9307055	0.91[JPT][hapmap]
rs9307061	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs9991237	0.84[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90033600-90052200	Weak transcription	Aorta	Aorta
2	chr4:90044800-90056000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:90046000-90056200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:90047600-90055800	Weak transcription	Fetal Intestine Large	intestine
5	chr4:90050800-90059000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:90051000-90056000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr4:90051200-90051800	Enhancers	A549	lung
8	chr4:90051200-90052400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:90051200-90053000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:90051200-90056000	Weak transcription	NHLF	lung
11	chr4:90051400-90052200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:90051400-90055800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:90051400-90056000	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links