Variant report

Variant	rs4342086
Chromosome Location	chr3:101503765-101503766
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr3:101503599-101504375	HL-60	blood:	n/a	chr3:101503893-101503906 chr3:101504089-101504098 chr3:101503898-101503911
2	SPI1	chr3:101503675-101504190	HL-60	blood:	n/a	chr3:101503893-101503906 chr3:101504089-101504098 chr3:101503898-101503911

Variant related genes	Relation type
NXPE3	TF binding region

Extended variants
information (count: 78 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1031710	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11706494	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11706986	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11707250	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11711903	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712309	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11712748	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap]
rs11712888	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11714278	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11714444	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11716558	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11717046	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11717638	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11718446	0.90[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.89[MKK][hapmap];0.81[YRI][hapmap]
rs11720745	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11914318	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11919389	0.96[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12631513	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12633089	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12633770	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13059470	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13060963	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13065944	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs13066768	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13068350	0.85[EUR][1000 genomes]
rs13069443	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs13077925	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13078652	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13081846	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs13084113	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13084432	0.84[EUR][1000 genomes]
rs13085776	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13094753	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13094911	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13099674	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1460097	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17347156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17347644	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17411983	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs1963961	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1963962	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2288272	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]
rs2290859	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2318090	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3094296	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.89[MEX][hapmap]
rs3094297	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs34063583	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34161138	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34181125	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34263427	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34376498	0.89[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.80[JPT][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34648996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34743741	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34883763	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34947019	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34963630	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35117343	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35315807	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35799195	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35810977	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35850993	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36002990	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3762729	0.80[JPT][hapmap]
rs3804775	0.80[JPT][hapmap]
rs3806653	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs3806654	0.92[CEU][hapmap];0.86[CHB][hapmap]
rs55859364	0.81[ASN][1000 genomes]
rs58658478	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61396602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62284198	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62284199	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7629753	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap]
rs7651721	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap]
rs9830943	0.92[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap]
rs997739	0.80[JPT][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
rs4342086	ZBTB11	cis	cerebellum	SCAN
rs4342086	NXPE3	cis	Esophagus Muscularis	GTEx
rs4342086	NIT2	cis	parietal	SCAN
rs4342086	FAM55C	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101498800-101504400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:101498800-101508200	Weak transcription	Placenta	Placenta
3	chr3:101498800-101519000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:101498800-101533800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:101498800-101546200	Weak transcription	Esophagus	oesophagus
6	chr3:101499000-101504200	Weak transcription	Colonic Mucosa	Colon
7	chr3:101499000-101513200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:101499000-101523000	Weak transcription	Stomach Mucosa	stomach
9	chr3:101499000-101533000	Weak transcription	Fetal Intestine Large	intestine
10	chr3:101499200-101529600	Weak transcription	Small Intestine	intestine
11	chr3:101499400-101510600	Weak transcription	Fetal Kidney	kidney
12	chr3:101499800-101512200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:101499800-101524800	Weak transcription	HepG2	liver
14	chr3:101500000-101509400	Weak transcription	Fetal Intestine Small	intestine
15	chr3:101500400-101504000	Weak transcription	Fetal Brain Male	brain
16	chr3:101500400-101508000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:101500400-101508000	Weak transcription	GM12878-XiMat	blood
18	chr3:101500400-101511800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:101500600-101504200	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:101500600-101511000	Strong transcription	HSMM	muscle
21	chr3:101501200-101507000	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:101501200-101507400	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr3:101501200-101510800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:101501200-101511000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:101501200-101516200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:101501400-101506600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:101501400-101506600	Strong transcription	Fetal Muscle Trunk	muscle
28	chr3:101501400-101507000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:101501400-101507200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:101501400-101509600	Strong transcription	Primary B cells from peripheral blood	blood
31	chr3:101501400-101511200	Strong transcription	Fetal Muscle Leg	muscle
32	chr3:101501600-101504200	Genic enhancers	Brain Angular Gyrus	brain
33	chr3:101501600-101504600	Strong transcription	Gastric	stomach
34	chr3:101501600-101504800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:101501600-101504800	Genic enhancers	Primary T cells fromperipheralblood	blood
36	chr3:101501600-101504800	Strong transcription	Ovary	ovary
37	chr3:101501600-101504800	Strong transcription	Pancreas	Pancrea
38	chr3:101501600-101504800	Strong transcription	HMEC	breast
39	chr3:101501600-101505000	Strong transcription	Right Ventricle	heart
40	chr3:101501600-101505200	Strong transcription	NHLF	lung
41	chr3:101501600-101505400	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr3:101501600-101505400	Strong transcription	Aorta	Aorta
43	chr3:101501600-101506600	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr3:101501600-101506600	Strong transcription	Fetal Stomach	stomach
45	chr3:101501600-101506800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:101501600-101507200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:101501600-101507200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:101501600-101507200	Strong transcription	Stomach Smooth Muscle	stomach
49	chr3:101501600-101510200	Strong transcription	Osteobl	bone
50	chr3:101501600-101511000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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