Variant report

Variant	rs16978509
Chromosome Location	chr18:43580729-43580730
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:43580506..43582779-chr18:43587364..43589939,2	K562	blood:
2	chr18:43580716..43582929-chr18:43614441..43616520,2	K562	blood:
3	chr18:43577618..43580480-chr18:43580513..43583485,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10468858	0.85[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs10468859	0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs10468860	0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs10468978	0.85[ASN][1000 genomes]
rs10468980	0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs12604893	0.84[EUR][1000 genomes]
rs12607686	0.94[EUR][1000 genomes]
rs16978508	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16978517	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1837213	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2276196	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2276197	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2276199	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3745001	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs3844540	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3897646	0.92[EUR][1000 genomes]
rs486424	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]
rs488431	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4890612	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4890613	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4890614	0.82[JPT][hapmap]
rs55966192	0.99[ASN][1000 genomes]
rs567504	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs568448	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57141604	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs593664	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs596415	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs610186	0.86[JPT][hapmap]
rs6507659	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs6507661	0.85[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs654466	0.82[JPT][hapmap]
rs687526	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs688547	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7227161	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs7237813	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7240441	0.87[JPT][hapmap]
rs7242970	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs72642435	0.97[ASN][1000 genomes]
rs920295	0.91[EUR][1000 genomes]
rs9675392	0.91[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv2277	chr18:43543715-43588579	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16978509	EPG5	cis	Whole Blood	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43558800-43608000	Weak transcription	Pancreas	Pancrea
2	chr18:43560400-43582600	Weak transcription	Fetal Intestine Small	intestine
3	chr18:43560400-43597600	Weak transcription	Left Ventricle	heart
4	chr18:43560600-43591600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr18:43562400-43583200	Weak transcription	Lung	lung
6	chr18:43562600-43585600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr18:43563400-43592000	Weak transcription	Psoas Muscle	Psoas
8	chr18:43565400-43588800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr18:43565400-43590800	Weak transcription	Colon Smooth Muscle	Colon
10	chr18:43565600-43588800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr18:43567800-43588800	Weak transcription	NHEK	skin
12	chr18:43568000-43583200	Weak transcription	Esophagus	oesophagus
13	chr18:43568600-43596800	Weak transcription	Adipose Nuclei	Adipose
14	chr18:43568800-43588600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr18:43568800-43607800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr18:43569400-43588800	Weak transcription	Fetal Stomach	stomach
17	chr18:43570000-43583000	Weak transcription	Aorta	Aorta
18	chr18:43570200-43588800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr18:43571400-43622000	Weak transcription	Gastric	stomach
20	chr18:43572200-43582600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr18:43573800-43582000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr18:43574200-43582000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr18:43574200-43582600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr18:43574200-43590000	Weak transcription	HMEC	breast
25	chr18:43574200-43592000	Weak transcription	NH-A	brain
26	chr18:43574200-43593200	Weak transcription	NHDF-Ad	bronchial
27	chr18:43574200-43597400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr18:43574200-43608000	Weak transcription	NHLF	lung
29	chr18:43574600-43608000	Weak transcription	Osteobl	bone
30	chr18:43576000-43585800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr18:43576600-43581600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr18:43576600-43588800	Weak transcription	Ovary	ovary
33	chr18:43577000-43581200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr18:43577000-43589600	Weak transcription	Liver	Liver
35	chr18:43578200-43581600	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr18:43578400-43581400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr18:43578400-43581600	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr18:43578600-43581200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr18:43578600-43581400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr18:43578600-43581600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr18:43578600-43582200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr18:43578600-43587200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr18:43579000-43587200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr18:43579000-43588600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr18:43579200-43580800	Weak transcription	Primary T cells from cord blood	blood
46	chr18:43579200-43581200	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr18:43579200-43582200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr18:43579200-43587200	Weak transcription	Spleen	Spleen
49	chr18:43579600-43580800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr18:43579600-43582000	Weak transcription	Primary hematopoietic stem cells	blood

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