Variant report

Variant	rs4517962
Chromosome Location	chr2:233578337-233578338
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1022330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1044480	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10933409	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10933411	0.83[EUR][1000 genomes]
rs10933412	0.83[EUR][1000 genomes]
rs11555646	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11676216	0.82[EUR][1000 genomes]
rs11679079	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11687128	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11690474	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11692545	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12472839	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12474040	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12478564	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12694917	0.83[EUR][1000 genomes]
rs12987513	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12990821	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12991088	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12997185	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13003675	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13004406	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13007783	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13008942	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13011298	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13013142	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13021246	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13024793	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13035829	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13424351	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1446308	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1446311	0.83[EUR][1000 genomes]
rs1801251	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1867778	0.90[EUR][1000 genomes]
rs1947105	0.81[EUR][1000 genomes]
rs2012221	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2044449	0.81[EUR][1000 genomes]
rs2100053	0.81[EUR][1000 genomes]
rs2305137	0.83[EUR][1000 genomes]
rs2592102	0.81[EUR][1000 genomes]
rs2592105	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2592113	0.92[EUR][1000 genomes]
rs2674839	0.92[EUR][1000 genomes]
rs2675971	0.81[EUR][1000 genomes]
rs2675973	0.81[EUR][1000 genomes]
rs2675974	0.81[EUR][1000 genomes]
rs283468	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs283469	0.80[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs283471	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs283474	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs283475	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs283476	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs283477	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs283479	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs283480	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs283481	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs283484	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs283485	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs283486	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs33980184	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34880628	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35085837	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35212961	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35285732	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35362030	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35395584	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35621474	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36007169	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3816334	0.83[EUR][1000 genomes]
rs3817311	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4452130	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4458205	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4973053	0.93[EUR][1000 genomes]
rs4973054	0.83[EUR][1000 genomes]
rs56777991	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6437074	0.83[EUR][1000 genomes]
rs66549961	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67013068	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6714245	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6717841	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6724117	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6732136	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6733151	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6738386	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6739638	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745879	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6746294	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6747645	0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6748027	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6761324	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71421663	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs737028	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7558609	0.88[EUR][1000 genomes]
rs7562712	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7578299	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7587309	0.83[EUR][1000 genomes]
rs7589201	0.81[EUR][1000 genomes]
rs7591176	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7592717	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606090	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs778166	0.95[EUR][1000 genomes]
rs895430	0.81[EUR][1000 genomes]
rs9653383	0.93[EUR][1000 genomes]
rs9679089	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs983430	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs991873	0.83[EUR][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	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4517962	C2orf82	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233563800-233582600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:233564000-233579600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:233564000-233589000	Weak transcription	NH-A	brain
4	chr2:233564200-233596400	Weak transcription	NHLF	lung
5	chr2:233564200-233613000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:233564800-233592800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:233565000-233612200	Weak transcription	Fetal Brain Male	brain
8	chr2:233565200-233589800	Weak transcription	HMEC	breast
9	chr2:233565200-233602000	Weak transcription	HUVEC	blood vessel
10	chr2:233565200-233606400	Weak transcription	Stomach Mucosa	stomach
11	chr2:233565400-233580200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:233565400-233589800	Weak transcription	Hela-S3	cervix
13	chr2:233565400-233590000	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:233565600-233641000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:233566000-233578400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:233566000-233584600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:233566800-233612800	Weak transcription	Small Intestine	intestine
18	chr2:233568000-233604400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr2:233568200-233583800	Strong transcription	HepG2	liver
20	chr2:233568200-233585400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:233568400-233585000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr2:233569000-233582000	Weak transcription	Brain Anterior Caudate	brain
23	chr2:233569000-233585600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr2:233569200-233579600	Weak transcription	Brain Substantia Nigra	brain
25	chr2:233569200-233589000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr2:233569200-233590000	Weak transcription	NHDF-Ad	bronchial
27	chr2:233569200-233615000	Weak transcription	Colonic Mucosa	Colon
28	chr2:233569400-233581000	Weak transcription	Pancreas	Pancrea
29	chr2:233569400-233612800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:233569400-233615400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr2:233570400-233581200	Weak transcription	Psoas Muscle	Psoas
32	chr2:233570600-233593400	Weak transcription	Aorta	Aorta
33	chr2:233570800-233582400	Weak transcription	Spleen	Spleen
34	chr2:233571000-233579400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr2:233571200-233581200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:233571200-233582400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr2:233571200-233593600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:233571200-233598200	Weak transcription	Fetal Kidney	kidney
39	chr2:233571200-233627400	Weak transcription	Gastric	stomach
40	chr2:233571400-233581000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:233571400-233582400	Weak transcription	Left Ventricle	heart
42	chr2:233571400-233585600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr2:233571400-233588600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:233571400-233601800	Weak transcription	Esophagus	oesophagus
45	chr2:233571600-233585600	Weak transcription	Right Ventricle	heart
46	chr2:233571600-233612200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr2:233572000-233579600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:233572200-233581600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr2:233572200-233585600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:233572200-233589000	Weak transcription	Osteobl	bone

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