Variant report

Variant	rs11229505
Chromosome Location	chr11:58274155-58274156
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr11:58274131-58274791	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000255299	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10792172	0.88[LWK][hapmap];0.82[YRI][hapmap]
rs10896774	0.87[AMR][1000 genomes]
rs10896775	0.85[AMR][1000 genomes]
rs10896785	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10896787	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10896788	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10896794	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10896795	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10896796	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11229409	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs11229410	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11229411	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11229412	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11229413	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11229423	0.83[AMR][1000 genomes]
rs11229463	0.83[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs11229512	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11229519	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11229543	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11229545	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11229555	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11530830	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11601687	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11603890	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11605269	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11605297	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11605683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12269745	0.87[AMR][1000 genomes]
rs12274866	0.87[AMR][1000 genomes]
rs12279895	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs12280114	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs12283414	0.87[AMR][1000 genomes]
rs12285111	0.83[CEU][hapmap];0.84[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes]
rs12286421	0.87[AMR][1000 genomes]
rs12289198	0.87[AMR][1000 genomes]
rs12290089	0.87[AMR][1000 genomes]
rs12291551	0.87[AMR][1000 genomes]
rs12294062	0.87[AMR][1000 genomes]
rs12786744	0.89[AMR][1000 genomes]
rs12787765	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12797488	0.89[AMR][1000 genomes]
rs12799215	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12800710	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12802819	0.87[AMR][1000 genomes]
rs12802960	0.87[AMR][1000 genomes]
rs12803648	0.83[AMR][1000 genomes]
rs12808544	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17474373	0.89[AMR][1000 genomes]
rs17567523	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1893902	0.83[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs1938598	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1938637	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs1986404	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes]
rs2000486	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2275993	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2276153	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2298608	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3168135	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35279927	0.87[AMR][1000 genomes]
rs4127353	0.84[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs4323891	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs4347409	0.87[AMR][1000 genomes]
rs4506677	0.87[AMR][1000 genomes]
rs4517537	0.87[AMR][1000 genomes]
rs4519112	0.80[AMR][1000 genomes]
rs4579945	0.87[AMR][1000 genomes]
rs6591475	0.83[CEU][hapmap];0.84[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes]
rs7102510	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7102852	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7110210	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7925560	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7927966	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7931394	0.87[AMR][1000 genomes]
rs8373	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

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	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv3403130	chr11:58273895-58274158	Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11229505	OR4C6	cis	cerebellum	SCAN
rs11229505	MS4A10	cis	cerebellum	SCAN
rs11229505	SERPING1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58262600-58274800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr11:58266800-58274800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr11:58266800-58278600	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr11:58266800-58278800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr11:58267000-58279600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr11:58269400-58277200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr11:58271000-58276400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr11:58273400-58275200	Enhancers	GM12878-XiMat	blood

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