Variant report

Variant	rs2515214
Chromosome Location	chr8:99808718-99808719
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	chr8:99808268..99810825-chr8:99820563..99822919,2	K562	blood:
2	chr8:99792612..99794533-chr8:99808664..99811217,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240870	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10447977	0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10755896	0.95[MEX][hapmap];0.88[TSI][hapmap]
rs10755897	0.95[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs10955189	0.82[AMR][1000 genomes]
rs10955190	0.82[CHB][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11774463	0.95[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes]
rs11778767	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11780292	0.81[AMR][1000 genomes]
rs11780369	0.81[AMR][1000 genomes]
rs11780500	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12114834	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12541317	0.95[CHB][hapmap];0.86[AMR][1000 genomes]
rs12547297	0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes]
rs12549803	0.87[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes]
rs12550783	0.95[MEX][hapmap];0.93[TSI][hapmap]
rs12679734	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12680195	0.82[CHB][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs13269932	0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes]
rs13275915	0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes]
rs13279438	0.88[AMR][1000 genomes]
rs1447245	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap]
rs1476181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1961744	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2028975	0.85[EUR][1000 genomes]
rs2442010	0.89[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2442011	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2442012	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2442013	0.86[EUR][1000 genomes]
rs2442014	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2442015	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs2515215	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2515216	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2515219	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2515221	0.85[EUR][1000 genomes]
rs2515224	0.94[EUR][1000 genomes]
rs2515225	0.81[EUR][1000 genomes]
rs2922066	0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs2922073	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2922074	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2922075	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2922076	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2922078	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2922081	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2922082	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3019290	0.85[AMR][1000 genomes]
rs3019291	0.85[AMR][1000 genomes]
rs3019293	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34281206	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34366206	0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34855977	0.89[AMR][1000 genomes]
rs35536167	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35798019	0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35804297	0.81[ASN][1000 genomes]
rs35915594	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4131873	0.82[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4255105	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4279561	0.82[CHB][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes]
rs4292660	0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4304299	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4413739	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4440607	0.88[AMR][1000 genomes]
rs4517094	0.82[CHB][hapmap];0.87[AMR][1000 genomes]
rs4541872	0.85[AMR][1000 genomes]
rs4549741	0.82[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes]
rs4562286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4612309	0.87[AMR][1000 genomes]
rs4734410	0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes]
rs4734417	0.82[EUR][1000 genomes]
rs4735568	0.91[MEX][hapmap];0.93[TSI][hapmap]
rs4735570	0.88[TSI][hapmap];0.81[AMR][1000 genomes]
rs4735571	0.86[AMR][1000 genomes]
rs4735574	0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes]
rs57034072	0.86[AMR][1000 genomes]
rs58321500	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62532565	0.86[AMR][1000 genomes]
rs62532577	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62532587	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62535408	0.80[AMR][1000 genomes]
rs62535410	0.84[AMR][1000 genomes]
rs62535412	0.86[AMR][1000 genomes]
rs6988087	0.89[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs6992925	0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs7818828	0.87[MEX][hapmap];0.83[TSI][hapmap]
rs7827435	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7838239	0.95[CHB][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7845271	0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9656842	0.93[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891218	chr8:99507313-99906221	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1027025	chr8:99672977-100115315	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv539690	chr8:99672977-100115315	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv891220	chr8:99681858-99867419	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	nsv1025685	chr8:99706280-99826236	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv539691	chr8:99706280-99826236	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv1031089	chr8:99715785-100399935	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv981968	chr8:99794499-99809509	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2515214	STK3	cis	parietal	SCAN
rs2515214	RGS22	cis	cerebellum	SCAN
rs2515214	OSR2	cis	cerebellum	SCAN
rs2515214	NCALD	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99797600-99809200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr8:99797600-99809200	Weak transcription	Pancreas	Pancrea
3	chr8:99797800-99809200	Weak transcription	Ovary	ovary
4	chr8:99805200-99808800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr8:99806000-99810200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr8:99806400-99811000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr8:99807200-99814000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr8:99808000-99809400	Weak transcription	K562	blood
9	chr8:99808200-99809200	Enhancers	NHEK	skin
10	chr8:99808200-99809600	Enhancers	GM12878-XiMat	blood
11	chr8:99808400-99809800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr8:99808400-99809800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr8:99808400-99810000	Enhancers	NHDF-Ad	bronchial
14	chr8:99808400-99810200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr8:99808600-99809200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr8:99808600-99809600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr8:99808600-99809600	Enhancers	HSMMtube	muscle
18	chr8:99808600-99809800	Enhancers	Muscle Satellite Cultured Cells	--
19	chr8:99808600-99809800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr8:99808600-99809800	Enhancers	HMEC	breast
21	chr8:99808600-99809800	Enhancers	Osteobl	bone

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