Variant report

Variant	rs62284199
Chromosome Location	chr3:101478531-101478532
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:101477002..101478820-chr3:101490149..101492423,2	MCF-7	breast:

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1031710	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	0.84[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	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11712309	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11712748	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	0.84[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	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11720745	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11914318	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11919389	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	0.95[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	0.82[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	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13066768	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	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	0.91[ASN][1000 genomes]
rs13084113	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	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13094753	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	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17347156	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	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	0.91[ASN][1000 genomes]
rs2290859	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	0.91[ASN][1000 genomes]
rs3094297	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]
rs34376498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	0.97[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	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]
rs3806653	0.92[ASN][1000 genomes]
rs3806654	0.92[ASN][1000 genomes]
rs3864012	0.86[ASN][1000 genomes]
rs4342086	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]
rs6768327	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs71625262	0.87[ASN][1000 genomes]
rs7628866	0.82[ASN][1000 genomes]
rs7629753	0.91[ASN][1000 genomes]
rs7645391	0.82[ASN][1000 genomes]
rs7651406	0.88[ASN][1000 genomes]
rs7651721	0.91[ASN][1000 genomes]
rs9830943	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62284199	RP11-49I4.3	cis	Esophagus Muscularis	GTEx
rs62284199	NXPE3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:122 , 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	chr3:101471800-101479400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:101472800-101478800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:101472800-101488400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:101473000-101478600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:101473000-101478600	Strong transcription	Fetal Lung	lung
9	chr3:101473000-101478600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr3:101473000-101478800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:101473000-101479000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:101473000-101479000	Strong transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:101473000-101479000	Strong transcription	HSMM	muscle
14	chr3:101473000-101479200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:101473000-101480800	Strong transcription	Fetal Muscle Trunk	muscle
16	chr3:101473000-101484400	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:101473000-101485400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:101473000-101485400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:101473000-101486000	Strong transcription	Dnd41	blood
20	chr3:101473200-101478800	Strong transcription	Fetal Stomach	stomach
21	chr3:101473200-101479200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:101473400-101478600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:101473400-101479000	Genic enhancers	Brain Hippocampus Middle	brain
24	chr3:101473400-101479200	Strong transcription	Left Ventricle	heart
25	chr3:101473400-101484600	Strong transcription	Fetal Thymus	thymus
26	chr3:101473600-101479200	Strong transcription	Primary hematopoietic stem cells	blood
27	chr3:101473600-101479400	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr3:101473800-101478600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr3:101473800-101478800	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr3:101473800-101479000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:101473800-101484600	Strong transcription	Primary B cells from peripheral blood	blood
32	chr3:101473800-101487200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr3:101474000-101478600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:101474000-101478600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:101474000-101479200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:101474000-101479200	Strong transcription	Primary B cells from cord blood	blood
37	chr3:101474000-101479200	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:101474000-101481200	Strong transcription	Fetal Brain Female	brain
39	chr3:101474000-101484400	Strong transcription	Thymus	Thymus
40	chr3:101474200-101478600	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr3:101474200-101478600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:101474200-101478600	Strong transcription	Fetal Intestine Large	intestine
43	chr3:101474200-101478600	Strong transcription	HepG2	liver
44	chr3:101474200-101479000	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr3:101474200-101479200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:101474200-101479200	Strong transcription	Duodenum Mucosa	Duodenum
47	chr3:101474200-101479400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:101474200-101480400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:101474200-101483000	Strong transcription	Brain Germinal Matrix	brain
50	chr3:101474200-101484400	Strong transcription	Primary T cells from cord blood	blood

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