Variant report

Variant	rs13065944
Chromosome Location	chr3:101473088-101473089
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:101445300..101447876-chr3:101472535..101474338,2	K562	blood:

Variant related genes	Relation type
ENSG00000182504	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1031710	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];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1056579	0.83[ASN][1000 genomes]
rs1138818	0.87[ASN][1000 genomes]
rs11706494	0.84[EUR][1000 genomes]
rs11706986	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11707250	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11710805	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11711079	0.86[ASN][1000 genomes]
rs11711903	0.91[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs11712309	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11712748	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.86[ASN][1000 genomes]
rs11712888	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11714278	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11714444	0.91[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11716558	0.84[EUR][1000 genomes]
rs11717046	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11717638	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11718446	0.85[JPT][hapmap]
rs11720745	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11914318	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11919389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[ASN][1000 genomes]
rs11924013	0.83[ASN][1000 genomes]
rs11925001	0.86[ASN][1000 genomes]
rs12631513	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12633089	0.91[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12636557	0.86[ASN][1000 genomes]
rs13059470	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.89[ASN][1000 genomes]
rs13060963	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13061565	0.86[ASN][1000 genomes]
rs13066768	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];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13068350	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13069443	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.85[ASN][1000 genomes]
rs13077703	0.86[ASN][1000 genomes]
rs13077925	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13078652	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13081846	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.86[ASN][1000 genomes]
rs13084113	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13084432	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13085776	0.81[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13094753	0.91[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13094911	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13096323	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13099674	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13100262	0.84[ASN][1000 genomes]
rs1460097	0.91[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17345528	0.90[JPT][hapmap]
rs17347156	0.96[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.85[EUR][1000 genomes]
rs17347644	0.83[EUR][1000 genomes]
rs17411983	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.87[ASN][1000 genomes]
rs1963961	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1963962	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2288272	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]
rs2290859	0.91[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2303474	0.86[ASN][1000 genomes]
rs2318090	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3094295	0.86[ASN][1000 genomes]
rs3094296	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.86[ASN][1000 genomes]
rs3094297	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.87[ASN][1000 genomes]
rs3109756	0.86[ASN][1000 genomes]
rs34063583	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34161138	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34181125	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34263427	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34301719	0.85[ASN][1000 genomes]
rs34376498	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]
rs34624546	0.86[ASN][1000 genomes]
rs34648996	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34743741	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34883763	0.88[ASN][1000 genomes]
rs34947019	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34963630	0.85[EUR][1000 genomes]
rs35117343	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];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35315807	0.83[EUR][1000 genomes]
rs35799195	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35810977	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35850993	1.00[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];0.91[ASN][1000 genomes]
rs36002990	0.91[ASN][1000 genomes]
rs3762729	0.90[JPT][hapmap]
rs3804775	0.90[JPT][hapmap]
rs3804778	0.90[JPT][hapmap]
rs3806653	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];0.87[ASN][1000 genomes]
rs3806654	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs3864012	0.80[ASN][1000 genomes]
rs4342086	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]
rs55654108	0.86[ASN][1000 genomes]
rs55821257	0.82[ASN][1000 genomes]
rs55859364	0.88[ASN][1000 genomes]
rs56291106	0.86[ASN][1000 genomes]
rs58658478	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59596156	0.86[ASN][1000 genomes]
rs61396602	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62282218	0.86[ASN][1000 genomes]
rs62284198	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62284199	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6768327	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71625262	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];0.84[MEX][hapmap];0.89[TSI][hapmap];0.86[ASN][1000 genomes]
rs7651406	0.83[ASN][1000 genomes]
rs7651721	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]
rs9830943	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[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
rs13065944	NIT2	cis	parietal	SCAN
rs13065944	ZBTB11	cis	cerebellum	SCAN
rs13065944	RP11-49I4.3	cis	Esophagus Muscularis	GTEx
rs13065944	NXPE3	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	chr3:101451800-101476600	Weak transcription	Psoas Muscle	Psoas
3	chr3:101453400-101478400	Weak transcription	Small Intestine	intestine
4	chr3:101453800-101473600	Weak transcription	HSMMtube	muscle
5	chr3:101453800-101474200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:101453800-101487000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:101454000-101474000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:101454200-101474200	Weak transcription	HMEC	breast
9	chr3:101454600-101473400	Weak transcription	Hela-S3	cervix
10	chr3:101454600-101476400	Weak transcription	NHEK	skin
11	chr3:101454600-101476600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:101454800-101474200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:101454800-101476600	Weak transcription	A549	lung
14	chr3:101455200-101476600	Weak transcription	Pancreas	Pancrea
15	chr3:101455400-101473400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:101455400-101473400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:101455400-101474200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:101455400-101474200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr3:101455400-101474200	Weak transcription	Aorta	Aorta
20	chr3:101455400-101474200	Weak transcription	Brain Angular Gyrus	brain
21	chr3:101455400-101474200	Weak transcription	Brain Substantia Nigra	brain
22	chr3:101455400-101474200	Weak transcription	Colonic Mucosa	Colon
23	chr3:101455400-101474200	Weak transcription	Esophagus	oesophagus
24	chr3:101455400-101474200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:101455400-101474400	Weak transcription	Ovary	ovary
26	chr3:101455400-101474400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:101455400-101474600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:101455400-101476200	Weak transcription	NHLF	lung
29	chr3:101455400-101476600	Weak transcription	Right Ventricle	heart
30	chr3:101455400-101476600	Weak transcription	K562	blood
31	chr3:101455400-101477800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:101455600-101473400	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:101455600-101474000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:101455600-101474000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:101455600-101474000	Weak transcription	Thymus	Thymus
36	chr3:101455600-101474200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:101455600-101474200	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr3:101455600-101474200	Weak transcription	GM12878-XiMat	blood
39	chr3:101455600-101476800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr3:101455800-101473400	Weak transcription	Left Ventricle	heart
41	chr3:101455800-101473800	Weak transcription	Primary B cells from peripheral blood	blood
42	chr3:101455800-101473800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr3:101455800-101473800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:101455800-101474000	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:101455800-101474000	Weak transcription	Placenta	Placenta
46	chr3:101455800-101474200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:101455800-101474200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:101455800-101474200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:101455800-101474200	Weak transcription	Adipose Nuclei	Adipose
50	chr3:101455800-101474200	Weak transcription	Liver	Liver

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