Variant report

Variant	rs2040644
Chromosome Location	chr12:47735480-47735481
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10492010	0.90[ASN][1000 genomes]
rs10492012	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183848	0.85[ASN][1000 genomes]
rs11183850	0.80[ASN][1000 genomes]
rs11183851	0.95[ASN][1000 genomes]
rs11183853	0.95[ASN][1000 genomes]
rs11183854	0.95[ASN][1000 genomes]
rs11183855	0.95[ASN][1000 genomes]
rs11183856	0.95[ASN][1000 genomes]
rs11183857	0.95[ASN][1000 genomes]
rs11183858	0.95[ASN][1000 genomes]
rs11183859	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11183860	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11183862	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11183863	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11183866	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11183869	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11183870	0.86[AMR][1000 genomes]
rs11183871	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11183872	0.90[ASN][1000 genomes]
rs11183874	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183875	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183877	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183878	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183879	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183880	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183881	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183882	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183883	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183884	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183885	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183886	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183890	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183891	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11183892	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183894	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183896	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183897	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183898	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183900	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183901	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183913	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183916	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183917	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183926	0.90[ASN][1000 genomes]
rs11183928	0.90[ASN][1000 genomes]
rs11183930	0.90[ASN][1000 genomes]
rs11183969	1.00[JPT][hapmap]
rs11561402	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12227067	0.90[ASN][1000 genomes]
rs12228428	0.85[ASN][1000 genomes]
rs12228708	0.90[ASN][1000 genomes]
rs12230585	0.85[ASN][1000 genomes]
rs12809861	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12809955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12810168	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12814166	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12814452	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817826	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818155	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818420	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12827137	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12832278	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12832953	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1833456	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040645	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040646	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2079026	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2079027	0.90[ASN][1000 genomes]
rs2079028	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs215340	0.88[CHB][hapmap];1.00[CHD][hapmap]
rs34187987	0.95[ASN][1000 genomes]
rs34692456	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34762197	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34878892	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35521464	0.90[ASN][1000 genomes]
rs35743720	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35839210	0.95[ASN][1000 genomes]
rs35889007	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs36059508	0.95[ASN][1000 genomes]
rs4473016	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4768145	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4768146	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4768147	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4768153	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4768796	0.86[AMR][1000 genomes]
rs4768797	0.86[AMR][1000 genomes]
rs4768798	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4768799	0.86[AMR][1000 genomes]
rs4768800	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4768805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71445736	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs71462954	0.85[ASN][1000 genomes]
rs71462956	0.90[ASN][1000 genomes]
rs71462957	0.90[ASN][1000 genomes]
rs71462959	0.90[ASN][1000 genomes]
rs71462960	0.90[ASN][1000 genomes]
rs71462961	0.90[ASN][1000 genomes]
rs855129	0.85[ASN][1000 genomes]
rs855131	0.85[ASN][1000 genomes]
rs855132	0.85[ASN][1000 genomes]
rs855133	0.85[ASN][1000 genomes]
rs855139	0.85[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	esv2751100	chr12:47541390-47746157	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv983319	chr12:47734799-47738693	Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2040644	YAF2	cis	parietal	SCAN
rs2040644	RHEBL1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47723200-47742200	Weak transcription	Primary T cells from cord blood	blood
2	chr12:47732400-47735600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr12:47734600-47737400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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