Variant report

Variant	rs62241297
Chromosome Location	chr3:20012343-20012344
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:20007751..20010574-chr3:20010896..20013275,2	MCF-7	breast:
2	chr3:20005781..20007385-chr3:20012300..20014395,2	K562	blood:
3	chr3:19986647..19989004-chr3:20010739..20012359,2	K562	blood:
4	chr3:19987383..19992426-chr3:20011245..20019650,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163576	Chromatin interaction
ENSG00000144566	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10222385	0.86[EUR][1000 genomes]
rs10510496	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11715597	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11717172	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12488378	0.90[AFR][1000 genomes]
rs12497083	0.90[EUR][1000 genomes]
rs17181086	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17181547	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17796169	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17796242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34914456	0.84[EUR][1000 genomes]
rs56070425	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56232690	0.82[EUR][1000 genomes]
rs62241269	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62241282	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62241284	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62241287	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62241288	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62241291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62241292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62241293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62241298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62241299	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62241315	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62241318	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62241319	0.92[EUR][1000 genomes]
rs62241320	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62241323	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62241325	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62280069	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6784536	0.84[EUR][1000 genomes]
rs6792745	0.84[EUR][1000 genomes]
rs6802632	0.84[EUR][1000 genomes]
rs9813641	0.89[EUR][1000 genomes]
rs9818225	0.86[EUR][1000 genomes]
rs9821831	0.82[EUR][1000 genomes]
rs9822455	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9827632	0.81[EUR][1000 genomes]
rs9828050	0.87[EUR][1000 genomes]
rs9828709	0.84[EUR][1000 genomes]
rs9834131	0.89[EUR][1000 genomes]
rs9838300	0.84[EUR][1000 genomes]
rs9838320	0.84[EUR][1000 genomes]
rs9854371	0.85[EUR][1000 genomes]
rs9855386	0.86[EUR][1000 genomes]
rs9858983	0.85[EUR][1000 genomes]
rs9871747	0.86[EUR][1000 genomes]
rs9882323	0.86[EUR][1000 genomes]
rs9882344	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
11	nsv997486	chr3:20006702-20113989	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs62241297	EFHB	cis	Stomach	GTEx
rs62241297	EFHB	cis	Muscle Skeletal	GTEx
rs62241297	EFHB	cis	Esophagus Mucosa	GTEx
rs62241297	EFHB	cis	Adipose Subcutaneous	GTEx
rs62241297	EFHB	cis	Skin Sun Exposed Lower leg	GTEx
rs62241297	EFHB	cis	Whole Blood	GTEx
rs62241297	EFHB	cis	Nerve Tibial	GTEx
rs62241297	EFHB	cis	Artery Tibial	GTEx
rs62241297	EFHB	cis	Esophagus Muscularis	GTEx

Chromatin state (count:125 , 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	chr3:19990000-20016200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:19990800-20017000	Weak transcription	Fetal Kidney	kidney
4	chr3:19991400-20017000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:19993600-20015600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:19993600-20023600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:19993800-20016200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:19993800-20023800	Weak transcription	Small Intestine	intestine
9	chr3:19994000-20015800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:19994000-20017400	Weak transcription	HSMMtube	muscle
11	chr3:19994600-20013800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:19995600-20017000	Weak transcription	Brain Germinal Matrix	brain
13	chr3:19995800-20016800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:19995800-20021800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:19996400-20017200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:19996400-20021000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:19996600-20015600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:19996600-20016800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr3:19997200-20013200	Weak transcription	HMEC	breast
20	chr3:19997200-20017000	Weak transcription	HUVEC	blood vessel
21	chr3:19997600-20015200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr3:19997800-20013200	Weak transcription	NHLF	lung
23	chr3:19997800-20015400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:19997800-20015600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:19997800-20016200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:19997800-20017000	Weak transcription	Brain Anterior Caudate	brain
27	chr3:19997800-20023200	Weak transcription	Spleen	Spleen
28	chr3:19998000-20017000	Weak transcription	HepG2	liver
29	chr3:19998200-20013200	Weak transcription	Osteobl	bone
30	chr3:19998400-20013200	Weak transcription	NHDF-Ad	bronchial
31	chr3:19998800-20013600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:19999000-20013400	Weak transcription	NH-A	brain
33	chr3:19999600-20027600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:20000800-20015600	Weak transcription	Fetal Lung	lung
35	chr3:20002200-20015600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:20002400-20013200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr3:20003800-20013000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:20003800-20013000	Weak transcription	NHEK	skin
39	chr3:20003800-20013400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:20003800-20013400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:20003800-20013600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:20003800-20015800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr3:20003800-20015800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:20003800-20015800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:20003800-20023600	Weak transcription	Aorta	Aorta
46	chr3:20004000-20015400	Weak transcription	Placenta	Placenta
47	chr3:20004000-20015600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr3:20004000-20020400	Weak transcription	Esophagus	oesophagus
49	chr3:20004400-20016200	Weak transcription	Fetal Brain Female	brain
50	chr3:20004600-20014600	Weak transcription	Right Atrium	heart

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