Variant report

Variant	rs6483969
Chromosome Location	chr11:10100734-10100735
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 181 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:178)

rs_ID	r²[population]
rs10160247	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10160669	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10160692	0.85[ASN][1000 genomes]
rs10500716	0.82[AMR][1000 genomes]
rs10500718	0.85[ASN][1000 genomes]
rs10500719	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10500720	0.89[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10500721	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs10500722	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs10500723	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs10770105	0.90[JPT][hapmap]
rs10840368	0.90[EUR][1000 genomes]
rs11042586	0.84[ASN][1000 genomes]
rs11042602	0.96[ASN][1000 genomes]
rs11042633	0.87[CEU][hapmap];0.92[EUR][1000 genomes]
rs11042650	0.85[ASN][1000 genomes]
rs11042652	0.83[ASN][1000 genomes]
rs11042653	0.83[ASN][1000 genomes]
rs11042656	0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11042657	0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11042659	0.82[ASN][1000 genomes]
rs11042661	0.82[ASN][1000 genomes]
rs11042663	0.82[ASN][1000 genomes]
rs11042664	0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11042666	0.93[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11042686	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs11042689	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs11042702	0.90[JPT][hapmap]
rs11042714	0.90[JPT][hapmap]
rs1135372	0.84[ASN][1000 genomes]
rs1135374	0.85[ASN][1000 genomes]
rs11821308	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs11825114	0.83[AMR][1000 genomes]
rs12224149	0.92[EUR][1000 genomes]
rs12274104	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12275224	0.82[ASN][1000 genomes]
rs12278680	0.94[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs12278735	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12280005	0.82[ASN][1000 genomes]
rs12281409	0.80[ASN][1000 genomes]
rs12281526	0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12282974	0.80[ASN][1000 genomes]
rs12284884	0.82[ASN][1000 genomes]
rs12286545	0.80[ASN][1000 genomes]
rs12286927	0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12287386	0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12288200	0.94[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12288275	0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12288486	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12288654	0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12291196	0.83[ASN][1000 genomes]
rs12291198	0.83[ASN][1000 genomes]
rs12291253	0.82[ASN][1000 genomes]
rs12293757	0.85[ASN][1000 genomes]
rs13377397	0.85[ASN][1000 genomes]
rs1442733	0.82[ASN][1000 genomes]
rs1442734	0.80[ASN][1000 genomes]
rs1442736	0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs16907334	0.84[AMR][1000 genomes]
rs16907407	0.80[AMR][1000 genomes]
rs16907410	0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16907417	0.82[CEU][hapmap];0.86[AMR][1000 genomes]
rs16907462	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16907471	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs16907481	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16907483	0.89[ASN][1000 genomes]
rs16907493	0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs16907496	0.85[ASN][1000 genomes]
rs16907498	0.85[ASN][1000 genomes]
rs16907500	0.85[ASN][1000 genomes]
rs16907503	0.85[ASN][1000 genomes]
rs16907504	0.94[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16907509	0.85[ASN][1000 genomes]
rs16907515	0.85[ASN][1000 genomes]
rs16907519	0.85[ASN][1000 genomes]
rs16907527	0.85[ASN][1000 genomes]
rs16907528	0.85[ASN][1000 genomes]
rs16907533	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs16907544	0.83[ASN][1000 genomes]
rs16907552	0.83[ASN][1000 genomes]
rs16907554	0.83[ASN][1000 genomes]
rs16907561	0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs16907564	0.82[ASN][1000 genomes]
rs16907568	0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs16907575	0.80[ASN][1000 genomes]
rs16907615	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs1822294	0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs1822295	0.94[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs1867136	0.82[ASN][1000 genomes]
rs1867137	0.93[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1867138	0.93[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2028575	0.85[ASN][1000 genomes]
rs2028576	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2028577	0.85[ASN][1000 genomes]
rs2028578	0.85[ASN][1000 genomes]
rs2069214	0.94[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2099877	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2119991	0.93[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2278628	0.85[ASN][1000 genomes]
rs2278630	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2278632	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2278633	0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs2278634	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs2403263	0.80[AMR][1000 genomes]
rs2403267	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2403290	0.90[ASN][1000 genomes]
rs2896513	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2896515	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2896517	0.86[AMR][1000 genomes]
rs3178898	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs34124136	0.87[ASN][1000 genomes]
rs34984386	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35815123	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4323860	0.90[JPT][hapmap]
rs4543988	0.85[ASN][1000 genomes]
rs4597056	0.85[JPT][hapmap]
rs4622247	0.85[ASN][1000 genomes]
rs4910115	0.90[JPT][hapmap]
rs56850765	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs57520536	0.90[ASN][1000 genomes]
rs57521137	0.83[ASN][1000 genomes]
rs57595438	0.82[ASN][1000 genomes]
rs57618276	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58652557	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58842960	0.97[ASN][1000 genomes]
rs60257382	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60319025	0.82[ASN][1000 genomes]
rs60578195	0.85[ASN][1000 genomes]
rs61149838	0.85[ASN][1000 genomes]
rs61520995	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61877012	0.84[AMR][1000 genomes]
rs61877040	0.80[ASN][1000 genomes]
rs61877045	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61878580	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61878581	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61878584	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61878585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61878625	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61878627	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61878628	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61878631	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61878632	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61878634	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6484012	0.86[ASN][1000 genomes]
rs6484147	0.90[JPT][hapmap]
rs6484148	0.90[JPT][hapmap]
rs6484152	0.90[JPT][hapmap]
rs7105321	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7107021	0.89[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs7107290	0.90[JPT][hapmap]
rs7108358	0.90[JPT][hapmap]
rs7110652	0.90[JPT][hapmap]
rs7113715	0.82[AMR][1000 genomes]
rs7118500	0.90[JPT][hapmap]
rs7122422	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs7123728	0.90[JPT][hapmap]
rs7124925	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7128234	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7129047	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7129531	0.83[CHB][hapmap]
rs721008	0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs726102	0.90[JPT][hapmap]
rs72860548	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73412899	0.85[ASN][1000 genomes]
rs73415015	0.85[ASN][1000 genomes]
rs7479039	0.90[JPT][hapmap]
rs7925889	0.85[JPT][hapmap]
rs7926678	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7930920	0.80[AMR][1000 genomes]
rs7931957	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7936409	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7938534	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938543	0.90[JPT][hapmap]
rs7938932	0.97[ASN][1000 genomes]
rs7939064	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7946649	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949164	0.83[AMR][1000 genomes]
rs9645625	0.81[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv553476	chr11:10024311-10117435	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6483969	RP11-351I24.1	cis	Whole Blood	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10072400-10101200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:10098200-10102600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr11:10098600-10101400	Weak transcription	Psoas Muscle	Psoas
4	chr11:10098600-10105400	Weak transcription	Left Ventricle	heart
5	chr11:10098600-10108400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr11:10098600-10121800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:10100400-10100800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr11:10100400-10100800	ZNF genes & repeats	Brain Substantia Nigra	brain
9	chr11:10100400-10101400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr11:10100400-10101600	ZNF genes & repeats	A549	lung
11	chr11:10100400-10102600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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