Variant report

Variant	rs3094295
Chromosome Location	chr3:101401995-101401996
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1031710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1056579	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1138818	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11706986	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11707250	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap]
rs11710533	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11710805	0.84[ASN][1000 genomes]
rs11711079	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711903	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.84[LWK][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs11712309	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11712748	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714278	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11714444	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.84[LWK][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs11717046	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11717638	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11718446	0.81[JPT][hapmap];0.80[LWK][hapmap]
rs11720745	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11914318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11917569	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11917682	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11919389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11923273	0.83[AMR][1000 genomes]
rs11924013	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11925001	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629658	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12629954	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12633089	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap]
rs12635128	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12636557	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639028	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13059470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13060963	0.87[ASN][1000 genomes]
rs13061565	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.86[ASN][1000 genomes]
rs13066768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.91[ASN][1000 genomes]
rs13068350	0.81[ASN][1000 genomes]
rs13069443	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13077703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077925	0.91[ASN][1000 genomes]
rs13081846	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082236	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13084113	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs13085776	0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap]
rs13094753	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.84[LWK][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs13096323	0.82[ASN][1000 genomes]
rs13099674	0.91[ASN][1000 genomes]
rs13100262	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1460097	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs17345528	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs17347156	0.96[CEU][hapmap];0.86[CHB][hapmap]
rs17411983	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1963961	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1963962	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2288272	1.00[ASW][hapmap];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[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290859	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.84[LWK][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs2303474	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2318090	0.91[ASN][1000 genomes]
rs3094296	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094297	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3109756	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34181125	0.91[ASN][1000 genomes]
rs34301719	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34376498	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.91[ASN][1000 genomes]
rs34624546	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34883763	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35117343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35850993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36002990	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36060163	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3762729	0.95[JPT][hapmap]
rs3804775	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs3804778	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs3806653	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3806654	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3864012	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4342086	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap]
rs55654108	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55821257	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55859364	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56291106	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59596156	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282218	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282255	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62284162	0.84[EUR][1000 genomes]
rs62284198	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62284199	0.91[ASN][1000 genomes]
rs71625262	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7629753	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7645391	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7651406	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7651721	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830943	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs997739	0.83[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3094295	NIT2	cis	parietal	SCAN
rs3094295	ZBTB11	cis	cerebellum	SCAN
rs3094295	RP11-49I4.3	cis	Esophagus Muscularis	GTEx
rs3094295	NXPE3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101396400-101402800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:101397000-101402400	Weak transcription	Fetal Brain Male	brain
3	chr3:101397000-101402600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:101397200-101402600	Weak transcription	Right Atrium	heart
5	chr3:101397200-101402600	Weak transcription	Right Ventricle	heart
6	chr3:101397200-101402800	Weak transcription	Fetal Heart	heart
7	chr3:101397400-101402000	Strong transcription	Fetal Intestine Small	intestine
8	chr3:101398400-101402000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:101398400-101402000	Strong transcription	Fetal Brain Female	brain
10	chr3:101398400-101402200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:101398400-101402600	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:101398400-101402600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:101398400-101402800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:101398400-101403400	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:101398600-101402200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:101398600-101402200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:101398600-101402200	Strong transcription	Fetal Muscle Leg	muscle
18	chr3:101398600-101402200	Strong transcription	Hela-S3	cervix
19	chr3:101398600-101402600	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr3:101398600-101402600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:101398600-101402600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:101398600-101402600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:101398600-101402600	Strong transcription	Duodenum Mucosa	Duodenum
24	chr3:101398600-101402600	Strong transcription	Fetal Lung	lung
25	chr3:101398600-101402600	Strong transcription	Placenta	Placenta
26	chr3:101398600-101402600	Strong transcription	Fetal Thymus	thymus
27	chr3:101398600-101402600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr3:101398600-101402800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:101398600-101403000	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr3:101398600-101403800	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr3:101398800-101402000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:101398800-101402000	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr3:101398800-101402000	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr3:101398800-101402000	Strong transcription	Brain Substantia Nigra	brain
35	chr3:101398800-101402000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr3:101398800-101402000	Strong transcription	HUVEC	blood vessel
37	chr3:101398800-101402200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:101398800-101402200	Strong transcription	Fetal Stomach	stomach
39	chr3:101398800-101402200	Strong transcription	Left Ventricle	heart
40	chr3:101398800-101402400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:101398800-101402400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr3:101398800-101402400	Strong transcription	Adipose Nuclei	Adipose
43	chr3:101398800-101402400	Strong transcription	HMEC	breast
44	chr3:101398800-101402600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:101398800-101402600	Strong transcription	Fetal Intestine Large	intestine
46	chr3:101398800-101402600	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr3:101398800-101402800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr3:101398800-101402800	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr3:101398800-101402800	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:101398800-101403000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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