Variant report

Variant	rs1862966
Chromosome Location	chr2:31254752-31254753
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	chr2:31247169..31249491-chr2:31252132..31255050,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10164479	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10166921	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10174368	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10192472	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10197865	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10198054	0.81[YRI][hapmap]
rs10206704	0.88[CEU][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10209881	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10210092	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10210124	0.96[CEU][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10210300	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10865086	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12473730	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12613732	0.87[MEX][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes]
rs12621546	0.81[ASW][hapmap];0.91[MEX][hapmap];0.80[YRI][hapmap]
rs12712300	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12712304	0.83[MEX][hapmap]
rs12999804	0.80[ASW][hapmap]
rs1862964	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1862965	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1862967	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1862968	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2113487	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2113488	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2161835	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2194454	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2194455	0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2194456	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2194457	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2216827	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2365191	0.96[ASN][1000 genomes]
rs4245766	0.95[JPT][hapmap]
rs4951959	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4951960	0.81[ASW][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes]
rs4952027	0.88[CEU][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4952028	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4952030	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4952031	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4952032	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4952033	0.87[ASN][1000 genomes]
rs4952038	0.83[ASN][1000 genomes]
rs5009910	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56284247	0.84[ASN][1000 genomes]
rs62140629	0.80[ASN][1000 genomes]
rs6543594	0.88[CEU][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6543595	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6708989	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6752071	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6752303	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6752662	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7558425	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7565923	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7579017	0.85[CEU][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7582401	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7592553	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7601904	0.88[CEU][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7605643	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7605982	0.81[YRI][hapmap];0.84[AMR][1000 genomes]
rs7608731	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9308914	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9679162	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1862966	SPAST	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31246400-31261600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr2:31251400-31270000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:31254000-31255200	Enhancers	GM12878-XiMat	blood
4	chr2:31254200-31256200	Enhancers	Primary B cells from cord blood	blood
5	chr2:31254400-31256200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr2:31254600-31256000	Enhancers	Spleen	Spleen
7	chr2:31254600-31256200	Enhancers	Primary monocytes fromperipheralblood	blood

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