Variant report

Variant	rs62241282
Chromosome Location	chr3:19993382-19993383
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:19993343-19993893	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:19986265-20000717	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:19992532..19994138-chr3:20013293..20015192,2	K562	blood:
2	chr3:19991110..19993492-chr3:20053410..20056377,2	K562	blood:
3	chr3:19971502..19973500-chr3:19993301..19994870,2	K562	blood:

Variant related genes	Relation type
EFHB	TF binding region
ENSG00000229468	Chromatin interaction
ENSG00000183977	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10222385	0.85[EUR][1000 genomes]
rs10510496	1.00[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	1.00[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]
rs62241284	1.00[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]
rs62241288	0.95[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:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv963301	chr3:19992240-19993486	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs62241282	EFHB	cis	Stomach	GTEx
rs62241282	EFHB	cis	Esophagus Muscularis	GTEx
rs62241282	EFHB	cis	Esophagus Mucosa	GTEx
rs62241282	EFHB	cis	Artery Tibial	GTEx
rs62241282	EFHB	cis	Skin Sun Exposed Lower leg	GTEx
rs62241282	EFHB	cis	Nerve Tibial	GTEx
rs62241282	EFHB	cis	Muscle Skeletal	GTEx
rs62241282	EFHB	cis	Whole Blood	GTEx
rs62241282	EFHB	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19989800-19995000	Weak transcription	Gastric	stomach
2	chr3:19989800-20018800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:19990000-19993400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr3:19990000-20008600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:19990000-20016200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:19990800-19996600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
7	chr3:19990800-20017000	Weak transcription	Fetal Kidney	kidney
8	chr3:19991000-19995200	Weak transcription	Brain Germinal Matrix	brain
9	chr3:19991000-19996200	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:19991000-19996600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:19991000-20001800	Weak transcription	Brain Angular Gyrus	brain
12	chr3:19991200-20002600	Weak transcription	Fetal Heart	heart
13	chr3:19991400-19993800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:19991400-19995000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:19991400-19995400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:19991400-19995400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:19991400-19998200	Weak transcription	Aorta	Aorta
18	chr3:19991400-19998800	Strong transcription	Fetal Thymus	thymus
19	chr3:19991400-20017000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:19991600-19995000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:19991600-19995400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:19991600-19997200	Strong transcription	NH-A	brain
23	chr3:19991600-19998400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:19991600-19998400	Weak transcription	Psoas Muscle	Psoas
25	chr3:19991600-20003800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:19991600-20003800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:19991800-19994400	Strong transcription	Fetal Lung	lung
28	chr3:19991800-19994600	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr3:19991800-19997600	Strong transcription	Primary B cells from peripheral blood	blood
30	chr3:19991800-19998000	Strong transcription	Fetal Intestine Large	intestine
31	chr3:19992000-19993400	Weak transcription	Fetal Brain Female	brain
32	chr3:19992000-19994200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr3:19992000-19994200	Strong transcription	Hela-S3	cervix
34	chr3:19992000-19994400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr3:19992000-19994600	Strong transcription	Brain Substantia Nigra	brain
36	chr3:19992000-19995400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
37	chr3:19992000-19995600	Weak transcription	Pancreas	Pancrea
38	chr3:19992000-19996200	Weak transcription	NHDF-Ad	bronchial
39	chr3:19992000-19998200	Strong transcription	K562	blood
40	chr3:19992000-20000000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr3:19992000-20000200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr3:19992000-20000400	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr3:19992000-20003400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr3:19992000-20004000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:19992200-19994000	Genic enhancers	Liver	Liver
46	chr3:19992200-19994600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr3:19992200-19996600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:19992200-19998400	Strong transcription	Placenta	Placenta
49	chr3:19992200-20001000	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr3:19992200-20012200	Weak transcription	Stomach Mucosa	stomach

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