Variant report

Variant	rs9532439
Chromosome Location	chr13:40369683-40369684
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11147769	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17591231	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17591266	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3812882	0.87[JPT][hapmap]
rs3812883	0.87[JPT][hapmap]
rs3812884	0.87[JPT][hapmap]
rs3812885	0.87[JPT][hapmap]
rs3812886	0.87[JPT][hapmap]
rs3812887	0.87[JPT][hapmap]
rs3812888	0.87[JPT][hapmap]
rs4142370	0.87[JPT][hapmap]
rs4245396	0.82[AMR][1000 genomes]
rs4312180	0.83[JPT][hapmap]
rs4338665	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4403927	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4408422	0.80[AMR][1000 genomes]
rs4409964	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4941936	0.95[JPT][hapmap]
rs4941937	0.87[JPT][hapmap]
rs4941938	0.87[JPT][hapmap]
rs4941939	0.83[JPT][hapmap]
rs4941941	0.83[JPT][hapmap]
rs4943686	0.87[JPT][hapmap]
rs4943694	0.80[AMR][1000 genomes]
rs4943695	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4943696	0.81[AMR][1000 genomes]
rs7319128	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7325068	0.91[CEU][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes]
rs7325655	0.87[JPT][hapmap]
rs7327779	0.87[JPT][hapmap]
rs7327824	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7332791	0.81[JPT][hapmap]
rs7334651	0.92[CEU][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap]
rs7337585	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7984113	0.87[JPT][hapmap]
rs8181861	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9315720	0.87[JPT][hapmap]
rs9315725	0.82[JPT][hapmap]
rs9315729	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9315730	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9532408	0.87[JPT][hapmap]
rs9532411	0.85[JPT][hapmap]
rs9532412	0.87[JPT][hapmap]
rs9532420	0.83[JPT][hapmap]
rs9532429	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9532432	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9532436	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9548857	0.87[JPT][hapmap]
rs9548859	0.87[JPT][hapmap]
rs9548862	0.87[JPT][hapmap]
rs9548863	0.87[JPT][hapmap]
rs9548865	0.87[JPT][hapmap]
rs9548866	0.87[JPT][hapmap]
rs9548867	0.87[JPT][hapmap]
rs9548868	0.87[JPT][hapmap]
rs9548869	0.87[JPT][hapmap]
rs9548875	0.83[JPT][hapmap]
rs9548880	0.83[JPT][hapmap]
rs9548901	0.92[CEU][hapmap];0.87[JPT][hapmap];0.84[YRI][hapmap];0.80[AMR][1000 genomes]
rs9548916	0.90[CEU][hapmap];0.83[YRI][hapmap]
rs9548917	0.91[CEU][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap]
rs9548919	0.91[CEU][hapmap];0.81[YRI][hapmap]
rs9548926	0.81[AMR][1000 genomes]
rs9548928	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9548929	0.82[AMR][1000 genomes]
rs9548930	0.91[CEU][hapmap];0.87[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9566474	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9576881	0.87[JPT][hapmap]
rs9576882	0.87[JPT][hapmap]
rs9576896	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9576897	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9576898	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9603617	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1054797	chr13:40198744-40618428	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv541755	chr13:40198744-40618428	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv832586	chr13:40222880-40379063	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1040458	chr13:40249387-40638129	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9532439	COG6	Cis_1M	lymphoblastoid	RTeQTL
rs9532439	COG6	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40364600-40377200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:40369000-40369800	Enhancers	Muscle Satellite Cultured Cells	--
3	chr13:40369000-40370200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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