Variant report

Variant	rs56193097
Chromosome Location	chr18:43468947-43468948
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10163872	0.90[ASN][1000 genomes]
rs10164218	0.90[ASN][1000 genomes]
rs1075906	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11082494	0.90[ASN][1000 genomes]
rs11082495	0.90[ASN][1000 genomes]
rs11082496	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1111937	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1115698	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1117868	0.90[ASN][1000 genomes]
rs1125807	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1440823	0.90[ASN][1000 genomes]
rs3744998	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4890305	0.90[ASN][1000 genomes]
rs4890604	0.87[ASN][1000 genomes]
rs4890605	0.90[ASN][1000 genomes]
rs55673821	0.90[ASN][1000 genomes]
rs56298801	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62095408	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7231317	0.84[ASN][1000 genomes]
rs8089685	0.90[ASN][1000 genomes]
rs967137	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9807578	0.90[ASN][1000 genomes]
rs9956058	0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525268	chr18:42748365-43474795	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56193097	EPG5	cis	Nerve Tibial	GTEx
rs56193097	EPG5	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43420200-43491800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr18:43429200-43473200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr18:43432000-43470400	Strong transcription	Adipose Nuclei	Adipose
4	chr18:43440600-43489600	Weak transcription	Small Intestine	intestine
5	chr18:43442400-43500200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr18:43445600-43478000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr18:43445800-43483800	Weak transcription	K562	blood
8	chr18:43446200-43479400	Weak transcription	Fetal Brain Male	brain
9	chr18:43447000-43478400	Weak transcription	Stomach Mucosa	stomach
10	chr18:43447000-43491800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr18:43447600-43469000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr18:43450800-43478000	Weak transcription	Right Ventricle	heart
13	chr18:43451800-43519600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr18:43452000-43479000	Weak transcription	HMEC	breast
15	chr18:43452400-43470400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr18:43453400-43470400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr18:43455000-43469000	Weak transcription	Colonic Mucosa	Colon
18	chr18:43455400-43511400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr18:43455600-43476400	Strong transcription	Primary T cells from cord blood	blood
20	chr18:43456000-43469200	Weak transcription	A549	lung
21	chr18:43456400-43469600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr18:43456400-43490200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr18:43456400-43498000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr18:43456400-43500400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr18:43456600-43473600	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr18:43457000-43470000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr18:43457200-43479200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr18:43457400-43471000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr18:43457600-43470000	Strong transcription	HSMMtube	muscle
30	chr18:43457600-43471000	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr18:43459200-43469000	Weak transcription	HUVEC	blood vessel
32	chr18:43459200-43478400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr18:43459200-43479200	Weak transcription	Psoas Muscle	Psoas
34	chr18:43460400-43471000	Strong transcription	Liver	Liver
35	chr18:43460600-43476000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr18:43460800-43473800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr18:43460800-43500200	Strong transcription	Osteobl	bone
38	chr18:43460800-43500400	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr18:43461000-43469000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr18:43461000-43478000	Weak transcription	Pancreas	Pancrea
41	chr18:43462200-43478000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr18:43462200-43492000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr18:43462400-43469000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr18:43462400-43477800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr18:43464000-43470000	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr18:43464800-43469000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr18:43464800-43469000	Weak transcription	Aorta	Aorta
48	chr18:43464800-43469000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr18:43464800-43469000	Weak transcription	Brain Substantia Nigra	brain
50	chr18:43464800-43469000	Weak transcription	Spleen	Spleen

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