Variant report

Variant	rs10519157
Chromosome Location	chr15:62381630-62381631
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:62363137..62365587-chr15:62379129..62382052,2	MCF-7	breast:
2	chr15:62368123..62372059-chr15:62380802..62384502,3	K562	blood:
3	chr15:62367214..62369987-chr15:62379884..62381677,2	MCF-7	breast:
4	chr15:62379222..62381891-chr15:62428344..62430839,2	MCF-7	breast:
5	chr15:62378815..62381663-chr15:62419269..62421288,2	MCF-7	breast:

Extended variants
information (count: 90 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10047986	0.87[EUR][1000 genomes]
rs1030859	0.86[EUR][1000 genomes]
rs10468026	0.86[EUR][1000 genomes]
rs11071642	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs11629596	0.88[EUR][1000 genomes]
rs11633500	0.87[EUR][1000 genomes]
rs11634163	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11635977	0.87[EUR][1000 genomes]
rs11635980	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11639482	0.81[CEU][hapmap]
rs12438690	0.87[EUR][1000 genomes]
rs12438803	0.87[EUR][1000 genomes]
rs12439356	0.88[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs12440524	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12442212	0.88[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs12442675	0.85[CEU][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs12592402	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs12594658	0.85[CEU][hapmap]
rs12898423	0.83[ASN][1000 genomes]
rs12908472	0.83[ASN][1000 genomes]
rs12912208	0.82[TSI][hapmap]
rs12913951	0.86[EUR][1000 genomes]
rs13379492	0.83[ASN][1000 genomes]
rs1344601	0.81[CEU][hapmap]
rs1436958	0.85[TSI][hapmap]
rs1436963	0.87[EUR][1000 genomes]
rs1436964	0.87[EUR][1000 genomes]
rs1436966	0.80[TSI][hapmap]
rs17205365	0.85[YRI][hapmap]
rs17205407	0.87[EUR][1000 genomes]
rs17205463	0.87[EUR][1000 genomes]
rs17238266	0.81[JPT][hapmap]
rs17271305	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17271340	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17271403	0.86[EUR][1000 genomes]
rs17271438	0.87[EUR][1000 genomes]
rs2162062	0.81[CEU][hapmap]
rs2414753	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs28411984	0.83[ASN][1000 genomes]
rs28513564	0.86[ASN][1000 genomes]
rs28542204	0.86[EUR][1000 genomes]
rs34096515	0.86[EUR][1000 genomes]
rs35967150	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3784633	0.83[CEU][hapmap]
rs3784634	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4143842	0.85[EUR][1000 genomes]
rs4143843	0.87[EUR][1000 genomes]
rs4564516	0.86[EUR][1000 genomes]
rs4587915	0.83[MEX][hapmap]
rs4774427	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.83[ASN][1000 genomes]
rs4775453	0.80[CEU][hapmap]
rs4775455	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs4775457	0.87[EUR][1000 genomes]
rs4775458	0.87[EUR][1000 genomes]
rs5006593	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs62008532	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7162536	0.87[EUR][1000 genomes]
rs7172967	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.83[ASN][1000 genomes]
rs7177173	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs7177276	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs7177711	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs7178424	0.88[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs7178540	0.88[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs7178945	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs7179506	0.82[ASN][1000 genomes]
rs731820	0.88[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs8025877	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs8026008	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs8027751	0.83[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs8029942	0.82[TSI][hapmap]
rs8032433	0.81[TSI][hapmap]
rs8034216	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8034335	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8034914	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[ASN][1000 genomes]
rs8038932	0.86[EUR][1000 genomes]
rs8039105	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8039651	0.85[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs893156	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs893158	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs933807	0.81[CEU][hapmap];0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457176	chr15:62178695-62519658	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv569643	chr15:62178695-62519658	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv471247	chr15:62202481-62519658	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv569646	chr15:62202482-62519658	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv1044748	chr15:62276183-62521856	Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv542405	chr15:62276183-62521856	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh 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	11 gene(s)	inside rSNPs	diseases
7	nsv457178	chr15:62340126-62394324	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv569652	chr15:62340126-62394324	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers 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	6 gene(s)	inside rSNPs	diseases
9	nsv1560	chr15:62354264-62399304	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv948606	chr15:62364932-63088916	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10519157	USP3	cis	cerebellum	SCAN
rs10519157	TPM1	cis	cerebellum	SCAN
rs10519157	VPS13C	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62379200-62382000	Enhancers	Pancreatic Islets	Pancreatic Islet
2	chr15:62379800-62382000	Enhancers	HUVEC	blood vessel
3	chr15:62380200-62381800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:62380200-62381800	Weak transcription	NHEK	skin
5	chr15:62380600-62382000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr15:62380800-62384400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:62381000-62384400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr15:62381200-62384800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links