Variant report

Variant	rs13099674
Chromosome Location	chr3:101489629-101489630
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	chr3:101484277..101486905-chr3:101489538..101492102,2	MCF-7	breast:

Extended variants
information (count: 111 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1031710	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];0.93[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	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11707250	0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11710805	0.83[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];0.83[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	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.91[ASN][1000 genomes]
rs11712888	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11714278	0.89[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];0.83[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	0.91[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];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11718446	0.85[JPT][hapmap]
rs11720745	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11914318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[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];0.84[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	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12635128	0.81[ASN][1000 genomes]
rs12636557	0.91[ASN][1000 genomes]
rs13059470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13060963	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13061565	0.91[ASN][1000 genomes]
rs13065944	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];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13066768	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];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13068350	0.81[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	0.95[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	0.88[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];0.83[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	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[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];0.87[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	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1963962	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2288272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][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	0.93[AFR][1000 genomes];0.97[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];0.91[ASN][1000 genomes]
rs3094297	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.92[ASN][1000 genomes]
rs3109756	0.89[ASN][1000 genomes]
rs34063583	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34161138	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34181125	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34263427	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34301719	0.87[ASN][1000 genomes]
rs34376498	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];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34624546	0.91[ASN][1000 genomes]
rs34648996	0.83[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	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35117343	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];0.91[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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];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	0.96[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];0.83[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	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62282218	0.91[ASN][1000 genomes]
rs62284198	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62284199	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768327	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs71625262	0.87[ASN][1000 genomes]
rs7628866	0.82[ASN][1000 genomes]
rs7629753	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.91[ASN][1000 genomes]
rs7645391	0.82[ASN][1000 genomes]
rs7651406	0.88[ASN][1000 genomes]
rs7651721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.91[ASN][1000 genomes]
rs9830943	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs997739	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv963500	chr3:101481412-101496033	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13099674	ZBTB11	cis	cerebellum	SCAN
rs13099674	NXPE3	cis	Esophagus Muscularis	GTEx
rs13099674	RP11-49I4.3	cis	Esophagus Muscularis	GTEx
rs13099674	NIT2	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101445600-101497400	Weak transcription	Fetal Heart	heart
2	chr3:101474800-101490600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:101477200-101497400	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:101477400-101497600	Weak transcription	Right Ventricle	heart
5	chr3:101477600-101497400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:101478000-101497400	Weak transcription	NHEK	skin
7	chr3:101478600-101489800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:101478600-101497400	Weak transcription	A549	lung
9	chr3:101478600-101497400	Weak transcription	K562	blood
10	chr3:101478800-101490400	Weak transcription	Ovary	ovary
11	chr3:101479000-101497400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:101479200-101490000	Weak transcription	Fetal Kidney	kidney
13	chr3:101479200-101497400	Weak transcription	NHLF	lung
14	chr3:101480400-101497400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:101482000-101497400	Weak transcription	HUVEC	blood vessel
16	chr3:101483000-101491200	Weak transcription	HSMMtube	muscle
17	chr3:101483000-101497400	Weak transcription	Brain Germinal Matrix	brain
18	chr3:101483200-101497400	Weak transcription	Fetal Intestine Small	intestine
19	chr3:101483800-101497200	Weak transcription	Fetal Stomach	stomach
20	chr3:101484200-101497400	Weak transcription	Brain Angular Gyrus	brain
21	chr3:101484200-101497400	Weak transcription	Hela-S3	cervix
22	chr3:101484200-101497400	Weak transcription	NHDF-Ad	bronchial
23	chr3:101484400-101489800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:101484400-101495800	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr3:101484400-101496400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:101484400-101497000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:101484400-101497200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:101484400-101497200	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:101484400-101497200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:101484400-101497200	Weak transcription	Fetal Muscle Leg	muscle
31	chr3:101484400-101497400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:101484400-101497400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:101484400-101497400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:101484400-101497400	Weak transcription	Brain Substantia Nigra	brain
35	chr3:101484400-101497400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr3:101484400-101497400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr3:101484400-101497400	Weak transcription	NH-A	brain
38	chr3:101484400-101497400	Weak transcription	Osteobl	bone
39	chr3:101484400-101497600	Weak transcription	Liver	Liver
40	chr3:101484400-101497600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr3:101484400-101497600	Weak transcription	Left Ventricle	heart
42	chr3:101484400-101497600	Weak transcription	Lung	lung
43	chr3:101484600-101490000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:101484600-101491000	Weak transcription	Fetal Brain Female	brain
45	chr3:101484600-101497400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:101484600-101497800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:101485400-101497400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:101485400-101497400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:101485400-101497400	Weak transcription	Adipose Nuclei	Adipose
50	chr3:101485400-101497600	Weak transcription	Placenta	Placenta

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