Variant report

Variant	rs34376498
Chromosome Location	chr3:101480156-101480157
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	chr3:101479888..101482048-chr3:101567660..101569894,2	K562	blood:

Variant related genes	Relation type
ENSG00000144802	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1031710	0.81[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];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1056579	0.89[ASN][1000 genomes]
rs1138818	0.92[ASN][1000 genomes]
rs11706494	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11706986	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11707250	0.89[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11710805	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11711079	0.91[ASN][1000 genomes]
rs11711903	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11712309	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11712748	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.91[ASN][1000 genomes]
rs11712888	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11714278	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11714444	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11716558	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11717046	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11717638	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11718446	0.85[JPT][hapmap];0.83[MKK][hapmap]
rs11720745	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11914318	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11919389	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]
rs11924013	0.88[ASN][1000 genomes]
rs11925001	0.91[ASN][1000 genomes]
rs12629954	0.82[ASN][1000 genomes]
rs12631513	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12633089	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12633770	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12635128	0.81[ASN][1000 genomes]
rs12636557	0.91[ASN][1000 genomes]
rs13059470	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13060963	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13061565	0.91[ASN][1000 genomes]
rs13065944	0.81[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];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13066768	0.81[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];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13068350	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13069443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.90[ASN][1000 genomes]
rs13077703	0.91[ASN][1000 genomes]
rs13077925	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13078652	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13081846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.91[ASN][1000 genomes]
rs13084113	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13084432	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13085776	0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13094753	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13094911	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13096323	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13099674	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13100262	0.90[ASN][1000 genomes]
rs1460097	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17345528	0.90[JPT][hapmap]
rs17347156	0.96[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17347644	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17411983	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.92[ASN][1000 genomes]
rs1963961	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1963962	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2288272	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]
rs2290859	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2303474	0.91[ASN][1000 genomes]
rs2318090	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094295	0.91[ASN][1000 genomes]
rs3094296	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.91[ASN][1000 genomes]
rs3094297	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.92[ASN][1000 genomes]
rs3109756	0.89[ASN][1000 genomes]
rs34063583	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34161138	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34181125	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34263427	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34301719	0.87[ASN][1000 genomes]
rs34624546	0.91[ASN][1000 genomes]
rs34648996	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34743741	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34883763	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34947019	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34963630	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35117343	0.81[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];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35315807	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35799195	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35810977	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35850993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36002990	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36060163	0.82[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];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.92[ASN][1000 genomes]
rs3806654	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs3864012	0.86[ASN][1000 genomes]
rs4342086	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]
rs55654108	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55821257	0.81[ASN][1000 genomes]
rs55859364	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56291106	0.91[ASN][1000 genomes]
rs58658478	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59596156	0.91[ASN][1000 genomes]
rs61396602	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62282218	0.91[ASN][1000 genomes]
rs62284198	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62284199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768327	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs71625262	0.87[ASN][1000 genomes]
rs7628866	0.82[ASN][1000 genomes]
rs7629753	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.91[ASN][1000 genomes]
rs7645391	0.82[ASN][1000 genomes]
rs7651406	0.88[ASN][1000 genomes]
rs7651721	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]
rs9830943	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs997739	0.90[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
rs34376498	ZBTB11	cis	cerebellum	SCAN
rs34376498	NIT2	cis	parietal	SCAN
rs34376498	NXPE3	cis	Esophagus Muscularis	GTEx
rs34376498	RP11-49I4.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101445600-101497400	Weak transcription	Fetal Heart	heart
2	chr3:101453800-101487000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:101464200-101486400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:101472800-101488400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:101473000-101480800	Strong transcription	Fetal Muscle Trunk	muscle
6	chr3:101473000-101484400	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:101473000-101485400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:101473000-101485400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:101473000-101486000	Strong transcription	Dnd41	blood
10	chr3:101473400-101484600	Strong transcription	Fetal Thymus	thymus
11	chr3:101473800-101484600	Strong transcription	Primary B cells from peripheral blood	blood
12	chr3:101473800-101487200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:101474000-101481200	Strong transcription	Fetal Brain Female	brain
14	chr3:101474000-101484400	Strong transcription	Thymus	Thymus
15	chr3:101474200-101480400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:101474200-101483000	Strong transcription	Brain Germinal Matrix	brain
17	chr3:101474200-101484400	Strong transcription	Primary T cells from cord blood	blood
18	chr3:101474200-101484400	Strong transcription	Fetal Muscle Leg	muscle
19	chr3:101474400-101485200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:101474800-101490600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:101475000-101483800	Weak transcription	Hela-S3	cervix
22	chr3:101475000-101486400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:101475600-101485800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:101475600-101488200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:101475800-101482800	Weak transcription	Fetal Intestine Small	intestine
26	chr3:101477000-101487200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr3:101477200-101480200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:101477200-101497400	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:101477400-101480400	Weak transcription	Brain Angular Gyrus	brain
30	chr3:101477400-101480400	Weak transcription	NHDF-Ad	bronchial
31	chr3:101477400-101481400	Weak transcription	Fetal Brain Male	brain
32	chr3:101477400-101486400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr3:101477400-101486600	Weak transcription	Esophagus	oesophagus
34	chr3:101477400-101497600	Weak transcription	Right Ventricle	heart
35	chr3:101477600-101482200	Weak transcription	GM12878-XiMat	blood
36	chr3:101477600-101482200	Weak transcription	HSMMtube	muscle
37	chr3:101477600-101483800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr3:101477600-101484000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:101477600-101486000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:101477600-101486000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:101477600-101488400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:101477600-101488400	Weak transcription	Spleen	Spleen
43	chr3:101477600-101497400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:101477800-101481600	Weak transcription	Osteobl	bone
45	chr3:101477800-101487800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:101478000-101480400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:101478000-101481400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr3:101478000-101482200	Weak transcription	Aorta	Aorta
49	chr3:101478000-101482600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:101478000-101483600	Weak transcription	Rectal Mucosa Donor 29	rectum

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