Variant report

Variant	rs61486882
Chromosome Location	chr2:55395578-55395579
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55240924..55243759-chr2:55395356..55397522,2	K562	blood:
2	chr2:55273899..55278013-chr2:55394987..55400290,7	K562	blood:
3	chr2:55241591..55242697-chr2:55395415..55396418,7	MCF-7	breast:
4	chr2:55391168..55392772-chr2:55394267..55395800,2	MCF-7	breast:
5	chr2:55291031..55292984-chr2:55393872..55396324,2	K562	blood:
6	chr2:55275046..55275830-chr2:55395421..55396072,2	MCF-7	breast:
7	chr2:55394216..55396855-chr2:55401149..55403821,2	K562	blood:
8	chr2:55275912..55276843-chr2:55395409..55396337,3	MCF-7	breast:
9	chr2:55241818..55242793-chr2:55395477..55396356,4	MCF-7	breast:
10	chr2:55126697..55127637-chr2:55395567..55396788,4	K562	blood:
11	chr2:55275783..55278013-chr2:55394198..55397050,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction
ENSG00000200086	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17046778	0.84[ASN][1000 genomes]
rs57681837	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs59439819	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs61109509	0.83[ASN][1000 genomes]
rs6726380	0.81[ASN][1000 genomes]
rs7349360	0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7349405	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7568777	0.80[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	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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs61486882	CLHC1	cis	Artery Tibial	GTEx
rs61486882	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL
rs61486882	CLHC1	cis	Muscle Skeletal	GTEx
rs61486882	CLHC1	cis	Thyroid	GTEx
rs61486882	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL
rs61486882	CLHC1	cis	Artery Aorta	GTEx
rs61486882	CLHC1	cis	Whole Blood	GTEx
rs61486882	C2orf63	cis	multi-tissue	Pritchard
rs61486882	CLHC1	cis	Nerve Tibial	GTEx
rs61486882	CLHC1	cis	lung	GTEx
rs61486882	CLHC1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55383600-55395600	Enhancers	Pancreas	Pancrea
2	chr2:55386800-55416600	Weak transcription	Esophagus	oesophagus
3	chr2:55387400-55395600	Enhancers	Lung	lung
4	chr2:55389200-55397400	Enhancers	NHLF	lung
5	chr2:55389800-55396000	Enhancers	Fetal Muscle Leg	muscle
6	chr2:55390000-55395600	Enhancers	Ovary	ovary
7	chr2:55390400-55395600	Enhancers	Right Atrium	heart
8	chr2:55390600-55395800	Enhancers	K562	blood
9	chr2:55391000-55397000	Enhancers	Brain Angular Gyrus	brain
10	chr2:55391200-55397000	Enhancers	NHDF-Ad	bronchial
11	chr2:55391400-55395800	Enhancers	Stomach Mucosa	stomach
12	chr2:55392000-55397400	Enhancers	HSMM	muscle
13	chr2:55392200-55395800	Enhancers	Adipose Nuclei	Adipose
14	chr2:55392800-55400400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:55393000-55404000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:55393000-55422000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr2:55393200-55395600	Weak transcription	Colonic Mucosa	Colon
18	chr2:55393400-55396200	Enhancers	Muscle Satellite Cultured Cells	--
19	chr2:55394000-55419000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:55394400-55395600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:55394400-55395800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:55394400-55396200	Enhancers	Fetal Heart	heart
23	chr2:55394600-55395600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:55394600-55395600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:55394600-55395600	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr2:55394600-55395800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:55394600-55395800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:55394600-55395800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr2:55394600-55395800	Enhancers	Fetal Intestine Large	intestine
30	chr2:55394600-55395800	Enhancers	Fetal Stomach	stomach
31	chr2:55394600-55396200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:55394600-55396200	Enhancers	Rectal Smooth Muscle	rectum
33	chr2:55394600-55396200	Enhancers	A549	lung
34	chr2:55394600-55396400	Enhancers	Colon Smooth Muscle	Colon
35	chr2:55394600-55396400	Enhancers	Fetal Lung	lung
36	chr2:55394600-55397000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:55394800-55395600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:55394800-55395800	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr2:55394800-55395800	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr2:55394800-55395800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:55394800-55395800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:55394800-55395800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:55394800-55396000	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr2:55394800-55396000	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr2:55395000-55395600	Enhancers	Brain Germinal Matrix	brain
46	chr2:55395000-55395600	Enhancers	Left Ventricle	heart
47	chr2:55395000-55395800	Enhancers	H1 Cell Line	embryonic stem cell
48	chr2:55395000-55395800	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr2:55395000-55395800	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr2:55395000-55395800	Enhancers	Aorta	Aorta

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