Variant report

Variant	rs282536
Chromosome Location	chr3:56632072-56632073
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10049468	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11130537	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17235670	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2317134	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2317244	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2317252	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs282522	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282523	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs282528	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs282541	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234393	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4681734	0.85[ASN][1000 genomes]
rs4681933	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681945	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681980	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4681994	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4682000	0.88[ASN][1000 genomes]
rs55831745	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55938093	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56190096	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56204053	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6445801	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445803	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445804	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445810	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6778373	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6781056	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6781293	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6787227	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6792321	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6802498	0.85[ASN][1000 genomes]
rs6809499	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73079883	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73079884	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73079891	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73079902	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73081810	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73081811	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73081819	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73081823	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73081825	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73081851	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73081854	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617331	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619465	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7620259	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631662	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7637449	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642389	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9809309	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9833926	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835332	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839065	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9858568	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9875257	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9878373	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	esv2762329	chr3:56629678-56633892	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
5	esv2753446	chr3:56630460-56633660	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs282536	CCDC66	cis	Thyroid	GTEx
rs282536	ARHGEF3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 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	chr3:56616200-56633800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:56616400-56639400	Weak transcription	Lung	lung
16	chr3:56617200-56639200	Weak transcription	Thymus	Thymus
17	chr3:56617200-56639600	Weak transcription	Aorta	Aorta
18	chr3:56617400-56639800	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:56617400-56639800	Weak transcription	Dnd41	blood
20	chr3:56619200-56639600	Weak transcription	Gastric	stomach
21	chr3:56619200-56639800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:56623000-56639600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:56624800-56639600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:56624800-56639800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:56625200-56633200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr3:56625200-56639600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:56625200-56639600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:56625200-56639600	Weak transcription	HMEC	breast
29	chr3:56625200-56640000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:56625200-56640000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:56625200-56650400	Weak transcription	NHEK	skin
32	chr3:56625200-56653400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:56625600-56639600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:56626200-56633000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:56626400-56656200	Weak transcription	Stomach Mucosa	stomach
36	chr3:56626800-56633400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:56627000-56632600	Strong transcription	Liver	Liver
38	chr3:56627000-56632800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:56627000-56633000	Strong transcription	Fetal Intestine Large	intestine
40	chr3:56627200-56633800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:56627400-56634000	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr3:56627600-56639600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:56627800-56639800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:56627800-56640000	Weak transcription	GM12878-XiMat	blood
45	chr3:56628000-56638800	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr3:56628200-56632600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:56628200-56639600	Weak transcription	Brain Angular Gyrus	brain
48	chr3:56628200-56640000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr3:56628400-56639600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:56628400-56639800	Weak transcription	H1 Cell Line	embryonic stem cell

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