Variant report

Variant	rs486424
Chromosome Location	chr18:43591672-43591673
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:43590898..43593115-chr18:43599068..43601449,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10468858	0.82[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs10468859	0.82[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs10468860	0.94[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs10468978	0.82[ASN][1000 genomes]
rs10468980	0.89[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs12604893	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12607686	0.94[EUR][1000 genomes]
rs16978508	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16978509	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16978517	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1837213	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3745001	0.85[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs3897646	0.87[EUR][1000 genomes]
rs488431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4890612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4890613	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55966192	0.96[ASN][1000 genomes]
rs567504	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs568448	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57141604	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs593664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs596415	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs610186	0.80[JPT][hapmap]
rs6507659	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs6507661	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs687526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs688547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7237813	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7240441	0.86[JPT][hapmap]
rs72642435	0.94[ASN][1000 genomes]
rs920295	0.88[EUR][1000 genomes]
rs9675392	0.89[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064882	chr18:43558343-43687674	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543693	chr18:43558343-43687674	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1062024	chr18:43589516-43749410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv543694	chr18:43589516-43749410	Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs486424	EPG5	cis	Whole Blood	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43558800-43608000	Weak transcription	Pancreas	Pancrea
2	chr18:43560400-43597600	Weak transcription	Left Ventricle	heart
3	chr18:43563400-43592000	Weak transcription	Psoas Muscle	Psoas
4	chr18:43568600-43596800	Weak transcription	Adipose Nuclei	Adipose
5	chr18:43568800-43607800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr18:43571400-43622000	Weak transcription	Gastric	stomach
7	chr18:43574200-43592000	Weak transcription	NH-A	brain
8	chr18:43574200-43593200	Weak transcription	NHDF-Ad	bronchial
9	chr18:43574200-43597400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr18:43574200-43608000	Weak transcription	NHLF	lung
11	chr18:43574600-43608000	Weak transcription	Osteobl	bone
12	chr18:43580000-43592600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr18:43582200-43592600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr18:43583400-43607800	Weak transcription	Fetal Intestine Small	intestine
15	chr18:43583400-43608200	Weak transcription	Esophagus	oesophagus
16	chr18:43586200-43607600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr18:43586600-43592200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr18:43586600-43592400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr18:43587200-43599800	Weak transcription	Fetal Intestine Large	intestine
20	chr18:43588000-43607400	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr18:43588600-43591800	Weak transcription	HSMMtube	muscle
22	chr18:43589200-43599000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr18:43589200-43607800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr18:43590200-43593200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr18:43590200-43594800	Weak transcription	Liver	Liver
26	chr18:43590400-43591800	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr18:43590400-43592600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr18:43590400-43593600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr18:43590400-43594800	Weak transcription	Lung	lung
30	chr18:43590800-43600600	Weak transcription	K562	blood
31	chr18:43590800-43601600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr18:43590800-43607800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr18:43590800-43608000	Weak transcription	Primary T cells from cord blood	blood
34	chr18:43591000-43592800	Weak transcription	Fetal Stomach	stomach
35	chr18:43591000-43592800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr18:43591000-43594000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr18:43591000-43594000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr18:43591000-43594400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr18:43591000-43595000	Weak transcription	Aorta	Aorta
40	chr18:43591000-43595000	Weak transcription	Spleen	Spleen
41	chr18:43591000-43600000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr18:43591000-43606200	Weak transcription	HMEC	breast
43	chr18:43591000-43607800	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr18:43591000-43607800	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr18:43591000-43608000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr18:43591000-43608000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr18:43591000-43608000	Weak transcription	Ovary	ovary
48	chr18:43591200-43592000	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr18:43591200-43593600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr18:43591200-43595000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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