Variant report

Variant	rs2246132
Chromosome Location	chr6:146182515-146182516
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:146181195..146184700-chr6:146185441..146188238,3	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1011597	0.95[JPT][hapmap]
rs10223507	0.85[JPT][hapmap]
rs1062068	0.85[JPT][hapmap]
rs1070518	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10872580	0.95[JPT][hapmap]
rs12199362	0.95[JPT][hapmap];1.00[YRI][hapmap]
rs1337839	0.81[JPT][hapmap]
rs1337841	0.95[JPT][hapmap]
rs1415744	0.95[JPT][hapmap]
rs1415746	0.95[JPT][hapmap]
rs1415747	0.95[JPT][hapmap]
rs1890170	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1890171	0.95[JPT][hapmap]
rs1970306	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2050027	0.95[JPT][hapmap]
rs2064185	0.94[JPT][hapmap]
rs2142978	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2142980	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2206142	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2223411	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2224120	0.85[JPT][hapmap]
rs2235481	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.86[MKK][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2247666	0.85[JPT][hapmap]
rs2249386	0.85[JPT][hapmap]
rs2253654	0.85[JPT][hapmap]
rs2253757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2265470	0.81[ASN][1000 genomes]
rs2265475	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2814874	0.84[JPT][hapmap]
rs2814875	0.85[JPT][hapmap]
rs2814877	0.85[JPT][hapmap]
rs34541797	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3811102	0.95[JPT][hapmap];1.00[YRI][hapmap]
rs3924499	0.85[JPT][hapmap]
rs3924502	0.85[JPT][hapmap]
rs4075694	0.85[JPT][hapmap]
rs4280983	0.85[JPT][hapmap];0.94[YRI][hapmap]
rs4895683	0.95[JPT][hapmap]
rs4896837	0.95[JPT][hapmap]
rs4896838	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs62435775	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6570708	0.95[JPT][hapmap]
rs6570732	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6900175	0.92[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6901888	0.95[JPT][hapmap]
rs6906258	0.95[JPT][hapmap]
rs6906402	0.95[JPT][hapmap]
rs6912351	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6915718	0.95[JPT][hapmap]
rs6922507	0.85[JPT][hapmap]
rs6923545	0.85[JPT][hapmap]
rs6930154	0.95[JPT][hapmap]
rs697053	0.95[JPT][hapmap]
rs697054	0.95[JPT][hapmap]
rs697055	0.95[JPT][hapmap]
rs702304	0.95[JPT][hapmap]
rs702306	0.94[JPT][hapmap]
rs702307	0.95[JPT][hapmap]
rs702316	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs702318	0.92[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs702319	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs702322	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs702324	0.92[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7746618	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7752286	0.95[JPT][hapmap]
rs7753092	0.85[JPT][hapmap];0.94[YRI][hapmap]
rs7753273	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7753696	0.85[JPT][hapmap]
rs7753770	0.95[JPT][hapmap]
rs863820	0.85[JPT][hapmap]
rs9285508	0.92[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs9373467	0.82[EUR][1000 genomes]
rs9373475	0.95[JPT][hapmap]
rs9376961	0.95[JPT][hapmap]
rs9376965	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9376970	0.85[JPT][hapmap];0.94[YRI][hapmap]
rs9386136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9390343	0.81[JPT][hapmap]
rs9390356	0.95[JPT][hapmap]
rs9390365	0.85[JPT][hapmap]
rs9403739	0.92[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9403742	0.85[JPT][hapmap]
rs9403749	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs9403756	0.85[JPT][hapmap]
rs9485017	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9497395	0.81[JPT][hapmap]
rs9497403	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9497426	0.83[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap]
rs9497431	0.85[JPT][hapmap];0.94[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034226	chr6:146071068-146306942	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv830835	chr6:146145148-146287473	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2246132	SHPRH	cis	cerebellum	SCAN
rs2246132	EPM2A	cis	parietal	SCAN
rs2246132	SHPRH	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146172200-146202400	Weak transcription	Adipose Nuclei	Adipose
2	chr6:146177600-146204200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:146178200-146184200	Weak transcription	Primary B cells from cord blood	blood
4	chr6:146181200-146183000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:146181600-146182600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:146181800-146187600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr6:146182400-146186600	Weak transcription	Primary T cells from cord blood	blood
8	chr6:146182400-146196600	Weak transcription	Fetal Heart	heart

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