Variant report

Variant	rs282539
Chromosome Location	chr3:56636246-56636247
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10865997	0.82[AMR][1000 genomes]
rs12486047	0.82[AMR][1000 genomes]
rs12631156	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs282524	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs282526	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs282532	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs282533	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs282534	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs282537	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs282538	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs282543	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732513	0.83[ASN][1000 genomes]
rs4974218	0.82[AMR][1000 genomes]
rs4974222	0.82[AMR][1000 genomes]
rs66873962	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6769055	0.82[AMR][1000 genomes]
rs7640995	0.83[ASN][1000 genomes]
rs9822876	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9985317	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv460557	chr3:56594735-56661320	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv590362	chr3:56594735-56661320	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs282539	CCDC66	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
2	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
3	chr3:56592800-56644600	Weak transcription	Fetal Heart	heart
4	chr3:56600600-56640000	Weak transcription	NHLF	lung
5	chr3:56603200-56650400	Weak transcription	K562	blood
6	chr3:56603600-56640000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:56605600-56639600	Weak transcription	Pancreas	Pancrea
8	chr3:56605800-56639400	Weak transcription	Spleen	Spleen
9	chr3:56605800-56639600	Weak transcription	Esophagus	oesophagus
10	chr3:56606200-56650200	Weak transcription	Colonic Mucosa	Colon
11	chr3:56607800-56639800	Weak transcription	HSMMtube	muscle
12	chr3:56607800-56650200	Weak transcription	Psoas Muscle	Psoas
13	chr3:56609400-56638600	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:56616400-56639400	Weak transcription	Lung	lung
15	chr3:56617200-56639200	Weak transcription	Thymus	Thymus
16	chr3:56617200-56639600	Weak transcription	Aorta	Aorta
17	chr3:56617400-56639800	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:56617400-56639800	Weak transcription	Dnd41	blood
19	chr3:56619200-56639600	Weak transcription	Gastric	stomach
20	chr3:56619200-56639800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:56623000-56639600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:56624800-56639600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:56624800-56639800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:56625200-56639600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:56625200-56639600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:56625200-56639600	Weak transcription	HMEC	breast
27	chr3:56625200-56640000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:56625200-56640000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr3:56625200-56650400	Weak transcription	NHEK	skin
30	chr3:56625200-56653400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:56625600-56639600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:56626400-56656200	Weak transcription	Stomach Mucosa	stomach
33	chr3:56627600-56639600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:56627800-56639800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:56627800-56640000	Weak transcription	GM12878-XiMat	blood
36	chr3:56628000-56638800	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr3:56628200-56639600	Weak transcription	Brain Angular Gyrus	brain
38	chr3:56628200-56640000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:56628400-56639600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:56628400-56639800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:56628400-56640000	Weak transcription	Brain Anterior Caudate	brain
42	chr3:56628400-56640200	Weak transcription	Osteobl	bone
43	chr3:56628600-56640000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:56628600-56649600	Weak transcription	HepG2	liver
45	chr3:56629000-56639000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:56629000-56647400	Weak transcription	HUVEC	blood vessel
47	chr3:56629000-56648000	Weak transcription	NH-A	brain
48	chr3:56629600-56640000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:56629600-56640000	Weak transcription	Primary B cells from peripheral blood	blood
50	chr3:56629600-56648200	Weak transcription	NHDF-Ad	bronchial

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