Variant report

Variant	rs12490799
Chromosome Location	chr3:20084542-20084543
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:20082249..20087148-chr3:20090873..20095169,4	K562	blood:
2	chr3:20081096..20083250-chr3:20083860..20086560,3	MCF-7	breast:
3	chr3:20083177..20086049-chr3:20086105..20087867,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114166	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11709453	1.00[ASN][1000 genomes]
rs12485260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492466	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493354	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17626752	1.00[ASN][1000 genomes]
rs1915920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1915921	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365366	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802632	0.81[AMR][1000 genomes]
rs7652967	0.90[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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv834627	chr3:20068115-20227975	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12490799	EFHB	cis	Artery Tibial	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20082800-20085800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr3:20083000-20084600	Weak transcription	Small Intestine	intestine
3	chr3:20083000-20085000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr3:20083000-20098600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:20083200-20084600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:20083200-20084600	Weak transcription	Esophagus	oesophagus
7	chr3:20083200-20084800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:20083200-20084800	Weak transcription	Aorta	Aorta
9	chr3:20083200-20085000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:20083200-20086200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr3:20083200-20088600	Weak transcription	Ovary	ovary
12	chr3:20083400-20084600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:20083400-20084800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:20083400-20084800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:20083400-20084800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:20083400-20084800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:20083400-20084800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:20083400-20084800	Enhancers	Colonic Mucosa	Colon
19	chr3:20083400-20084800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:20083400-20084800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:20083400-20084800	Weak transcription	HUVEC	blood vessel
22	chr3:20083400-20085000	Enhancers	Primary B cells from peripheral blood	blood
23	chr3:20083400-20085000	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr3:20083400-20085000	Enhancers	Spleen	Spleen
25	chr3:20083400-20085400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:20083400-20085400	Enhancers	Pancreas	Pancrea
27	chr3:20083400-20085600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr3:20083400-20085600	Flanking Active TSS	Thymus	Thymus
29	chr3:20083400-20085800	Enhancers	Fetal Intestine Large	intestine
30	chr3:20083400-20086200	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr3:20083400-20086600	Enhancers	Placenta	Placenta
32	chr3:20083400-20089000	Weak transcription	Fetal Brain Male	brain
33	chr3:20083600-20084600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:20083600-20084600	Enhancers	Primary T cells fromperipheralblood	blood
35	chr3:20083600-20084600	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr3:20083600-20084600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr3:20083600-20084600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:20083600-20084600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:20083600-20084600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:20083600-20084600	Weak transcription	A549	lung
41	chr3:20083600-20084600	Enhancers	Dnd41	blood
42	chr3:20083600-20084600	Weak transcription	NHDF-Ad	bronchial
43	chr3:20083600-20084800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:20083600-20084800	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr3:20083600-20084800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:20083600-20084800	Enhancers	Adipose Nuclei	Adipose
47	chr3:20083600-20084800	Enhancers	Liver	Liver
48	chr3:20083600-20084800	Enhancers	Colon Smooth Muscle	Colon
49	chr3:20083600-20084800	Weak transcription	Right Ventricle	heart
50	chr3:20083600-20084800	Enhancers	Hela-S3	cervix

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