Variant report

Variant	rs13252069
Chromosome Location	chr8:51556084-51556085
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10101197	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10101893	0.94[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap]
rs10103285	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10104963	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10110936	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10111120	0.94[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs10111412	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10111994	0.84[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10216485	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10216995	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10808845	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10958003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10958014	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10958015	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10958020	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11779190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11786241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11991963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11997602	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13252090	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13254513	0.81[CHB][hapmap]
rs13254671	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13255182	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13255431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13259412	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13262678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1384831	0.94[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap]
rs1905377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1961173	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2063237	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2086768	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271204	0.93[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs2392706	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2392707	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs28705974	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28736522	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34433142	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4338122	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4367561	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4401874	0.93[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4424266	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4601323	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4607637	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66463531	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67095253	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6983093	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6993752	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7002596	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7006744	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs717511	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][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	nsv948436	chr8:51115028-51917504	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv429914	chr8:51371447-51617647	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv531502	chr8:51390997-51703556	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3514165	chr8:51416583-51923545	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv3514166	chr8:51416583-51923545	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv890873	chr8:51462163-51612641	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1027452	chr8:51525439-51725489	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv20833	chr8:51555987-51558277	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13252069	EFCAB1	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:51554800-51556800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr8:51555200-51556400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr8:51555200-51556600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr8:51555400-51556200	Weak transcription	Fetal Brain Female	brain
5	chr8:51555600-51556200	Enhancers	NH-A	brain
6	chr8:51555600-51556400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr8:51555600-51556600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr8:51555600-51556600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr8:51555600-51556600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr8:51555600-51556600	Flanking Active TSS	HUVEC	blood vessel
11	chr8:51555800-51556400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr8:51555800-51556600	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr8:51555800-51556800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr8:51556000-51556400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr8:51556000-51556400	Enhancers	Fetal Lung	lung
16	chr8:51556000-51556800	Enhancers	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links