Variant report

Variant	rs11919389
Chromosome Location	chr3:101424458-101424459
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:101414723..101417089-chr3:101422376..101424511,2	K562	blood:
2	chr3:101404286..101407235-chr3:101422427..101426148,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114391	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1031710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1056579	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1138818	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11706494	0.80[EUR][1000 genomes]
rs11706986	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11707250	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11710533	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11710805	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11711079	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11711903	0.96[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11712309	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11712748	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11712888	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11714278	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11714444	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11716558	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11717046	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11717638	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11718446	0.85[JPT][hapmap]
rs11720745	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11914318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11917569	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11917682	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11924013	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11925001	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12629658	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12629954	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12631513	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12633089	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs12635128	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12636557	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12639028	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13059470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13060963	0.90[ASN][1000 genomes]
rs13061565	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13065944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[ASN][1000 genomes]
rs13066768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13068350	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13069443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13077703	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13077925	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13078652	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13081846	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13082236	0.81[AMR][1000 genomes]
rs13084113	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs13084432	0.83[ASN][1000 genomes]
rs13085776	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13094753	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13094911	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13096323	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13099674	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13100262	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1460097	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17345528	0.90[JPT][hapmap]
rs17347156	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17411983	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1963961	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1963962	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2288272	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2290859	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2303474	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2318090	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3094295	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3094296	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3094297	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3109756	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34063583	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34161138	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34181125	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34263427	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34301719	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34376498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34624546	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34648996	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34743741	0.82[ASN][1000 genomes]
rs34883763	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34947019	0.82[ASN][1000 genomes]
rs34963630	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35117343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35315807	0.81[ASN][1000 genomes]
rs35799195	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35810977	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35850993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36002990	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36060163	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3762729	0.90[JPT][hapmap]
rs3804775	0.90[JPT][hapmap]
rs3804778	0.90[JPT][hapmap]
rs3806653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806654	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3864012	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4342086	0.96[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55654108	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55821257	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55859364	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56291106	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58658478	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59596156	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61396602	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62282218	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62282255	0.81[AMR][1000 genomes]
rs62284162	0.86[EUR][1000 genomes]
rs62284198	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62284199	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6768327	0.82[ASN][1000 genomes]
rs71625262	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7628866	0.80[ASN][1000 genomes]
rs7629753	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7645391	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7651406	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7651721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9830943	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs997739	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv963348	chr3:101424441-101434477	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11919389	NXPE3	cis	Esophagus Muscularis	GTEx
rs11919389	RP11-49I4.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101406600-101426400	Weak transcription	Fetal Intestine Small	intestine
2	chr3:101422400-101426000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:101422400-101427200	Weak transcription	Osteobl	bone
4	chr3:101422400-101427400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:101422600-101426200	Weak transcription	A549	lung
6	chr3:101422800-101430200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:101423800-101430000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:101423800-101430600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:101424000-101426000	Weak transcription	Placenta	Placenta

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