Variant report

Variant	rs62241288
Chromosome Location	chr3:20000228-20000229
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:19998852..20001425-chr3:20020103..20022422,2	MCF-7	breast:
2	chr3:19999505..20001254-chr3:20002139..20004557,2	MCF-7	breast:
3	chr3:19999385..20001229-chr3:20001451..20003044,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10222385	0.85[EUR][1000 genomes]
rs10510496	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11715597	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11717172	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12488378	0.84[AFR][1000 genomes]
rs12497083	0.89[EUR][1000 genomes]
rs17181086	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17181547	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17796169	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17796242	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34914456	0.83[EUR][1000 genomes]
rs56070425	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56232690	0.81[EUR][1000 genomes]
rs62241269	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62241282	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62241284	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62241287	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62241291	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62241292	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62241293	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62241297	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62241298	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62241299	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62241315	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62241318	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62241319	0.91[EUR][1000 genomes]
rs62241320	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62241323	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62241325	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs62280069	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6784536	0.83[EUR][1000 genomes]
rs6792745	0.83[EUR][1000 genomes]
rs6802632	0.83[EUR][1000 genomes]
rs9813641	0.88[EUR][1000 genomes]
rs9818225	0.85[EUR][1000 genomes]
rs9821831	0.81[EUR][1000 genomes]
rs9822455	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9828050	0.86[EUR][1000 genomes]
rs9828709	0.83[EUR][1000 genomes]
rs9834131	0.88[EUR][1000 genomes]
rs9838300	0.83[EUR][1000 genomes]
rs9838320	0.83[EUR][1000 genomes]
rs9854371	0.84[EUR][1000 genomes]
rs9855386	0.85[EUR][1000 genomes]
rs9858983	0.84[EUR][1000 genomes]
rs9871747	0.85[EUR][1000 genomes]
rs9882323	0.85[EUR][1000 genomes]
rs9882344	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs62241288	EFHB	cis	Artery Tibial	GTEx
rs62241288	EFHB	cis	Esophagus Mucosa	GTEx
rs62241288	EFHB	cis	Stomach	GTEx
rs62241288	EFHB	cis	Muscle Skeletal	GTEx
rs62241288	EFHB	cis	Esophagus Muscularis	GTEx
rs62241288	EFHB	cis	Adipose Subcutaneous	GTEx
rs62241288	EFHB	cis	Whole Blood	GTEx
rs62241288	EFHB	cis	Nerve Tibial	GTEx
rs62241288	EFHB	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19989800-20018800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:19990000-20008600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:19990000-20016200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:19990800-20017000	Weak transcription	Fetal Kidney	kidney
5	chr3:19991000-20001800	Weak transcription	Brain Angular Gyrus	brain
6	chr3:19991200-20002600	Weak transcription	Fetal Heart	heart
7	chr3:19991400-20017000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:19991600-20003800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:19991600-20003800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:19992000-20000400	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr3:19992000-20003400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:19992000-20004000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:19992200-20001000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:19992200-20012200	Weak transcription	Stomach Mucosa	stomach
15	chr3:19992400-20001000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:19992600-20000400	Strong transcription	HSMM	muscle
17	chr3:19992600-20003800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:19993600-20015600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:19993600-20023600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:19993800-20003600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:19993800-20016200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:19993800-20023800	Weak transcription	Small Intestine	intestine
23	chr3:19994000-20015800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:19994000-20017400	Weak transcription	HSMMtube	muscle
25	chr3:19994600-20011600	Weak transcription	Brain Substantia Nigra	brain
26	chr3:19994600-20013800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:19995000-20000600	Strong transcription	Fetal Intestine Small	intestine
28	chr3:19995000-20002400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:19995200-20000600	Strong transcription	GM12878-XiMat	blood
30	chr3:19995600-20017000	Weak transcription	Brain Germinal Matrix	brain
31	chr3:19995800-20016800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr3:19995800-20021800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:19996000-20002200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr3:19996400-20003200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
35	chr3:19996400-20003400	Weak transcription	Left Ventricle	heart
36	chr3:19996400-20003800	Weak transcription	Esophagus	oesophagus
37	chr3:19996400-20017200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr3:19996400-20021000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr3:19996600-20002000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr3:19996600-20003400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr3:19996600-20007200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:19996600-20015600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:19996600-20016800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr3:19996800-20002800	Weak transcription	Fetal Brain Female	brain
45	chr3:19996800-20007800	Weak transcription	Adipose Nuclei	Adipose
46	chr3:19997000-20003400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr3:19997200-20013200	Weak transcription	HMEC	breast
48	chr3:19997200-20017000	Weak transcription	HUVEC	blood vessel
49	chr3:19997600-20001400	Weak transcription	Primary B cells from peripheral blood	blood
50	chr3:19997600-20011800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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