Variant report

Variant	rs59439819
Chromosome Location	chr2:55432336-55432337
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs17046778	0.93[ASN][1000 genomes]
rs1821832	0.81[AMR][1000 genomes]
rs2576722	0.83[AMR][1000 genomes]
rs2920965	0.84[ASN][1000 genomes]
rs57529275	0.82[ASN][1000 genomes]
rs57681837	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59783675	0.91[AMR][1000 genomes]
rs61109509	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61486882	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6726380	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71414550	0.81[AMR][1000 genomes]
rs7349360	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7349405	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[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	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs59439819	CLHC1	cis	Artery Aorta	GTEx
rs59439819	CLHC1	cis	Muscle Skeletal	GTEx
rs59439819	CLHC1	cis	Esophagus Mucosa	GTEx
rs59439819	CLHC1	cis	Nerve Tibial	GTEx
rs59439819	CLHC1	cis	Thyroid	GTEx
rs59439819	CLHC1	cis	Esophagus Muscularis	GTEx
rs59439819	CLHC1	cis	Artery Tibial	GTEx
rs59439819	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL
rs59439819	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL
rs59439819	CLHC1	cis	Whole Blood	GTEx
rs59439819	CLHC1	cis	Stomach	GTEx
rs59439819	C2orf63	cis	multi-tissue	Pritchard
rs59439819	CLHC1	cis	lung	GTEx
rs59439819	CLHC1	cis	Heart Left Ventricle	GTEx
rs59439819	CLHC1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55397200-55450000	Weak transcription	NH-A	brain
2	chr2:55402800-55450000	Weak transcription	NHDF-Ad	bronchial
3	chr2:55415400-55450000	Weak transcription	GM12878-XiMat	blood
4	chr2:55416800-55450000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:55417400-55450200	Weak transcription	Placenta	Placenta
6	chr2:55417800-55439200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:55417800-55450000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:55418400-55433600	Weak transcription	Brain Anterior Caudate	brain
9	chr2:55419400-55434400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:55420400-55433800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:55420600-55433600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:55421000-55433600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:55423200-55438800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr2:55423800-55432800	Weak transcription	Pancreas	Pancrea
15	chr2:55423800-55448000	Weak transcription	HSMM	muscle
16	chr2:55424200-55432600	Weak transcription	HSMMtube	muscle
17	chr2:55424200-55432800	Weak transcription	NHEK	skin
18	chr2:55424200-55450000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:55424400-55434200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:55424400-55435000	Weak transcription	Osteobl	bone
21	chr2:55424400-55442200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:55424600-55442800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:55424600-55449800	Weak transcription	Thymus	Thymus
24	chr2:55424600-55450000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:55424600-55450200	Weak transcription	Brain Germinal Matrix	brain
26	chr2:55424600-55451200	Weak transcription	HepG2	liver
27	chr2:55424800-55434000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr2:55424800-55450200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:55425600-55449800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr2:55427400-55432600	Weak transcription	Fetal Stomach	stomach
31	chr2:55427400-55432600	Weak transcription	Lung	lung
32	chr2:55427400-55433800	Weak transcription	Fetal Thymus	thymus
33	chr2:55427400-55434200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr2:55427400-55450200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:55427400-55450200	Weak transcription	Aorta	Aorta
36	chr2:55427400-55450600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:55427400-55450600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:55428800-55434400	Weak transcription	Brain Hippocampus Middle	brain
39	chr2:55428800-55439400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr2:55429200-55433000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:55429200-55449800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:55430000-55437800	Weak transcription	Fetal Intestine Large	intestine
43	chr2:55430000-55443200	Weak transcription	Fetal Intestine Small	intestine
44	chr2:55430000-55450400	Weak transcription	Left Ventricle	heart
45	chr2:55430200-55433000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:55430400-55433000	Strong transcription	Primary T cells from cord blood	blood
47	chr2:55430400-55433000	Weak transcription	Fetal Muscle Leg	muscle
48	chr2:55430400-55433600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:55430800-55432600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:55430800-55433200	Weak transcription	Brain Cingulate Gyrus	brain

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