Variant report

Variant	rs11746701
Chromosome Location	chr5:52688918-52688919
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10805447	0.80[EUR][1000 genomes]
rs10805448	0.80[EUR][1000 genomes]
rs10805449	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10940313	0.80[EUR][1000 genomes]
rs10940315	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10940316	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11740065	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11740124	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11741680	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11741744	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11744360	0.80[EUR][1000 genomes]
rs11745979	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11746341	0.80[EUR][1000 genomes]
rs11746509	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11746732	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11748130	0.80[EUR][1000 genomes]
rs11748797	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11955043	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12153379	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12657880	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13156108	0.80[EUR][1000 genomes]
rs13162095	0.80[EUR][1000 genomes]
rs13163048	0.80[EUR][1000 genomes]
rs13167150	0.81[EUR][1000 genomes]
rs13167469	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13171352	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13171813	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13174717	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13175176	0.81[EUR][1000 genomes]
rs13175475	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13176442	0.81[EUR][1000 genomes]
rs13178720	0.80[EUR][1000 genomes]
rs13183277	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13188654	0.84[AMR][1000 genomes]
rs34256928	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34268497	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34547502	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34750307	0.80[EUR][1000 genomes]
rs34801686	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34924451	0.80[EUR][1000 genomes]
rs34942708	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34985749	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35152485	0.81[EUR][1000 genomes]
rs35201567	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35237162	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35314846	0.80[EUR][1000 genomes]
rs35573280	0.80[EUR][1000 genomes]
rs35586638	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35636180	0.80[EUR][1000 genomes]
rs35930552	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4131065	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4254864	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4274942	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4301187	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4326101	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4499786	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4535418	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4549480	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4568325	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55746953	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55793310	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55880944	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56285131	0.80[EUR][1000 genomes]
rs62357814	0.80[EUR][1000 genomes]
rs62357815	0.80[EUR][1000 genomes]
rs62357825	0.81[EUR][1000 genomes]
rs62357827	0.81[EUR][1000 genomes]
rs62357829	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62357837	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62357857	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62357858	0.86[AMR][1000 genomes]
rs62357859	0.86[AMR][1000 genomes]
rs62359260	0.89[AMR][1000 genomes]
rs62359263	0.86[AMR][1000 genomes];0.82[EUR][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	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv830297	chr5:52492494-52707758	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv508356	chr5:52646168-52703120	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11746701	NDUFS4	cis	parietal	SCAN
rs11746701	MOCS2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52688000-52689200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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