Variant report

Variant	rs11715835
Chromosome Location	chr3:48770732-48770733
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 120 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1048940	0.84[CEU][hapmap]
rs10780033	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11130176	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11705888	0.90[ASN][1000 genomes]
rs11706052	0.85[AMR][1000 genomes]
rs11706203	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11706983	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs11708022	1.00[AMR][1000 genomes]
rs11708786	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11709092	0.96[AMR][1000 genomes]
rs11709246	1.00[AMR][1000 genomes]
rs11713694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs11715177	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11715689	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11715713	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717978	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11719291	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs11719457	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11920534	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11928552	0.87[CHD][hapmap]
rs12107252	0.83[GIH][hapmap]
rs12107418	0.83[GIH][hapmap]
rs12493289	1.00[JPT][hapmap]
rs12493578	1.00[CHD][hapmap]
rs12497850	1.00[CHD][hapmap]
rs13063223	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13063312	0.83[GIH][hapmap]
rs13070798	0.83[GIH][hapmap];1.00[MEX][hapmap]
rs13072554	0.85[AMR][1000 genomes]
rs13073997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13074318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13080725	0.85[AMR][1000 genomes]
rs13084000	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13086240	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs13087930	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13090013	0.81[ASN][1000 genomes]
rs13090839	0.89[AMR][1000 genomes]
rs13092715	1.00[JPT][hapmap]
rs13094900	0.96[AMR][1000 genomes]
rs13316551	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13324142	0.83[GIH][hapmap]
rs13324950	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13434258	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs1352420	1.00[CHD][hapmap]
rs17080289	0.83[GIH][hapmap]
rs17080319	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2276850	0.83[GIH][hapmap]
rs2276852	0.83[GIH][hapmap]
rs2286652	0.83[GIH][hapmap];1.00[MEX][hapmap]
rs2310996	0.83[GIH][hapmap]
rs28567949	0.81[ASN][1000 genomes]
rs28657585	0.81[ASN][1000 genomes]
rs28793701	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34037363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes]
rs34153629	0.81[ASN][1000 genomes]
rs34477108	1.00[AMR][1000 genomes]
rs34504524	0.85[AMR][1000 genomes]
rs34509487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35064573	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs35102816	0.85[AMR][1000 genomes]
rs35108630	0.85[AMR][1000 genomes]
rs3774628	1.00[JPT][hapmap]
rs3821876	0.83[GIH][hapmap]
rs3923475	0.85[AMR][1000 genomes]
rs4077495	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4858798	1.00[CHD][hapmap]
rs4858828	1.00[CHD][hapmap]
rs4858831	1.00[CHD][hapmap]
rs4974079	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4974085	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4974087	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs55761431	0.85[AMR][1000 genomes]
rs56318350	0.90[AMR][1000 genomes]
rs56735597	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61729488	0.85[AMR][1000 genomes]
rs6442130	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6446253	1.00[JPT][hapmap]
rs67060340	0.96[AMR][1000 genomes]
rs67332931	1.00[AMR][1000 genomes]
rs6788650	1.00[CHD][hapmap]
rs6791542	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6792156	0.83[GIH][hapmap]
rs71324924	1.00[AMR][1000 genomes]
rs71324929	0.85[AMR][1000 genomes]
rs73078349	0.81[AMR][1000 genomes]
rs73078362	0.81[AMR][1000 genomes]
rs73080361	0.88[AMR][1000 genomes]
rs740787	0.83[GIH][hapmap]
rs7430501	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7431710	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7431857	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7623023	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7627404	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7631574	0.83[GIH][hapmap]
rs7647813	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7649458	1.00[CHD][hapmap]
rs9311430	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9311433	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9311434	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9637481	1.00[JPT][hapmap]
rs9682444	0.87[CHD][hapmap]
rs9755490	0.87[CHD][hapmap]
rs9811027	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs9811318	0.83[GIH][hapmap]
rs9812200	0.83[GIH][hapmap]
rs9830581	0.83[GIH][hapmap]
rs9834996	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9835307	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9836462	0.83[GIH][hapmap]
rs9841602	0.83[GIH][hapmap]
rs9843316	0.83[GIH][hapmap]
rs9850134	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9871180	0.83[GIH][hapmap]
rs9876848	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9877542	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9877685	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9881877	0.83[GIH][hapmap]
rs9882549	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9884022	1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs11715835	CCDC71	cis	cerebellum	SCAN
rs11715835	LRRC2	cis	cerebellum	SCAN
rs11715835	CSPG5	cis	parietal	SCAN
rs11715835	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs11715835	ARIH2	cis	cerebellum	SCAN
rs11715835	WDR6	cis	parietal	SCAN
rs11715835	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs11715835	WDR6	cis	Whole Blood	GTEx
rs11715835	WDR6	cis	cerebellum	SCAN
rs11715835	RNF123	cis	parietal	SCAN
rs11715835	WDR6	cis	Artery Tibial	GTEx
rs11715835	WDR6	cis	Adipose Subcutaneous	GTEx
rs11715835	CCDC36	cis	cerebellum	SCAN
rs11715835	KBTBD3	trans	parietal	SCAN
rs11715835	HEMK1	cis	parietal	SCAN
rs11715835	WDR6	cis	Esophagus Mucosa	GTEx
rs11715835	NICN1	cis	cerebellum	SCAN
rs11715835	C3orf62	cis	cerebellum	SCAN
rs11715835	ALAS1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48769800-48771000	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr3:48770000-48772800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:48770400-48770800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr3:48770600-48770800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:48770600-48770800	Enhancers	NHEK	skin
6	chr3:48770600-48771000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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