Variant report

Variant	rs11953554
Chromosome Location	chr5:42846876-42846877
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1035516	0.87[AMR][1000 genomes]
rs1046068	0.87[JPT][hapmap]
rs10462041	0.83[AMR][1000 genomes]
rs10941587	0.83[AMR][1000 genomes]
rs10941592	0.82[CEU][hapmap]
rs10941593	0.82[CEU][hapmap]
rs11952526	0.84[CEU][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes]
rs11958761	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12054838	0.81[AMR][1000 genomes]
rs12055266	0.83[AMR][1000 genomes]
rs12187996	0.83[JPT][hapmap]
rs12516954	0.80[AMR][1000 genomes]
rs12517112	0.87[JPT][hapmap]
rs12518414	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12519443	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12519532	0.82[CEU][hapmap]
rs12520759	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12521615	0.82[CEU][hapmap]
rs12522458	0.89[AMR][1000 genomes]
rs13178745	0.88[AMR][1000 genomes]
rs1364024	0.81[AMR][1000 genomes]
rs1364027	0.83[AMR][1000 genomes]
rs1423649	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1423651	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1423652	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2113086	0.82[CEU][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2161600	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs28919892	0.86[JPT][hapmap]
rs34417548	0.85[ASN][1000 genomes]
rs35896631	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797310	0.87[JPT][hapmap]
rs3849695	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3906418	0.83[AMR][1000 genomes]
rs4866799	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4866803	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4866804	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4866805	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4866806	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4866949	0.85[JPT][hapmap]
rs4866961	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4866966	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4866967	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs55651065	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs55687632	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs55688895	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs56394865	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs58394380	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59073137	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59184964	0.84[AFR][1000 genomes]
rs60008560	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs61099053	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61371942	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62370951	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62370953	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62370959	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6865453	0.82[CEU][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes]
rs6880056	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6882786	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6896902	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7579	0.86[JPT][hapmap]
rs7703376	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7708223	0.83[JPT][hapmap]
rs7719242	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7725776	0.82[JPT][hapmap]
rs7725961	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs7730190	0.87[JPT][hapmap]
rs7734918	0.81[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes]
rs7735857	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8180482	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs882775	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9687651	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv597886	chr5:42610409-42854408	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
5	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
6	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
7	nsv523033	chr5:42752037-42919685	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv965602	chr5:42767568-42889585	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
10	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
11	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
12	nsv1018276	chr5:42809131-42975245	Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11953554	CCDC152	cis	Artery Aorta	GTEx
rs11953554	CCDC152	cis	Artery Tibial	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42843800-42847000	Weak transcription	K562	blood
2	chr5:42844200-42847000	Weak transcription	Fetal Lung	lung
3	chr5:42844400-42851400	Weak transcription	Fetal Intestine Small	intestine
4	chr5:42846800-42847200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:42846800-42847200	Flanking Active TSS	HepG2	liver
6	chr5:42846800-42848000	Active TSS	Liver	Liver

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