Variant report

Variant	rs11706986
Chromosome Location	chr3:101455966-101455967
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1031710	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1056579	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1138818	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11706494	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11707250	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11710533	0.85[EUR][1000 genomes]
rs11710805	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11711079	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11711903	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11712309	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11712748	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11712888	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11714278	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11714444	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11716558	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11717046	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717638	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11720745	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11914318	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917569	0.86[EUR][1000 genomes]
rs11917682	0.86[EUR][1000 genomes]
rs11919389	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11924013	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11925001	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12629658	0.86[EUR][1000 genomes]
rs12629954	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12631513	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12633089	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12633770	0.80[AMR][1000 genomes]
rs12635128	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12636557	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12639028	0.82[EUR][1000 genomes]
rs13059470	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13060963	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13061565	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13065944	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13066768	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13068350	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13069443	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13077703	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13077925	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13078652	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13081846	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13084113	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13084432	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13085776	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13094753	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13094911	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13096323	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13099674	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13100262	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1460097	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17347156	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17347644	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17411983	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1963961	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1963962	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2288272	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2290859	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2303474	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2318090	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3094295	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3094296	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3094297	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3109756	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34063583	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34161138	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34181125	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34263427	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34301719	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34376498	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34624546	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34648996	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34743741	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34883763	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34947019	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34963630	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35117343	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35315807	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35799195	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35810977	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35850993	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36002990	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36060163	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3806653	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3806654	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3864012	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4342086	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55654108	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55821257	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55859364	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56291106	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58658478	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59596156	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61396602	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62282218	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62284198	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62284199	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6768327	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs71625262	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7628866	0.84[ASN][1000 genomes]
rs7629753	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7645391	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7651406	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7651721	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9830943	0.85[EUR][1000 genomes];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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11706986	NXPE3	cis	Esophagus Muscularis	GTEx
rs11706986	RP11-49I4.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101445600-101456400	Strong transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:101445600-101497400	Weak transcription	Fetal Heart	heart
3	chr3:101445800-101456200	Strong transcription	H1 Cell Line	embryonic stem cell
4	chr3:101445800-101456200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:101446200-101456000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:101448000-101456000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:101448400-101456200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:101449600-101456200	Strong transcription	Primary B cells from cord blood	blood
9	chr3:101449800-101456000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr3:101450200-101456000	Strong transcription	Duodenum Mucosa	Duodenum
11	chr3:101450200-101456600	Strong transcription	Primary T cells from cord blood	blood
12	chr3:101450800-101456000	Strong transcription	Stomach Smooth Muscle	stomach
13	chr3:101451200-101456600	ZNF genes & repeats	Fetal Brain Female	brain
14	chr3:101451400-101459600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:101451600-101463400	Weak transcription	HepG2	liver
16	chr3:101451800-101476600	Weak transcription	Psoas Muscle	Psoas
17	chr3:101452000-101456400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:101452800-101457600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:101453000-101456000	ZNF genes & repeats	Brain Germinal Matrix	brain
20	chr3:101453000-101456000	Strong transcription	Osteobl	bone
21	chr3:101453000-101458200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:101453400-101456000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:101453400-101456800	Weak transcription	Stomach Mucosa	stomach
24	chr3:101453400-101478400	Weak transcription	Small Intestine	intestine
25	chr3:101453600-101456800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:101453800-101456600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:101453800-101473600	Weak transcription	HSMMtube	muscle
28	chr3:101453800-101474200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:101453800-101487000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr3:101454000-101457400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr3:101454000-101458200	Weak transcription	NHDF-Ad	bronchial
32	chr3:101454000-101474000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:101454200-101458600	Weak transcription	NH-A	brain
34	chr3:101454200-101473000	Weak transcription	HSMM	muscle
35	chr3:101454200-101474200	Weak transcription	HMEC	breast
36	chr3:101454400-101456400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:101454400-101456600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:101454400-101464400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr3:101454600-101456000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:101454600-101456000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
41	chr3:101454600-101463800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:101454600-101473400	Weak transcription	Hela-S3	cervix
43	chr3:101454600-101476400	Weak transcription	NHEK	skin
44	chr3:101454600-101476600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr3:101454800-101456000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr3:101454800-101474200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr3:101454800-101476600	Weak transcription	A549	lung
48	chr3:101455000-101463600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr3:101455200-101456000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:101455200-101457400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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