Variant report

Variant	rs62366408
Chromosome Location	chr5:74053764-74053765
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1043968	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10515191	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1104272	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11739122	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11741464	0.80[ASN][1000 genomes]
rs11741789	0.88[EUR][1000 genomes]
rs11741825	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11742460	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11742621	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11742773	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11743655	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11746611	0.80[ASN][1000 genomes]
rs11746702	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11746757	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11747965	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11749137	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11948188	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11955898	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1350097	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1447453	0.88[EUR][1000 genomes]
rs15694	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16872297	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16872299	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16872333	0.85[EUR][1000 genomes]
rs16872346	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16872347	0.85[EUR][1000 genomes]
rs16872364	0.85[EUR][1000 genomes]
rs17852781	0.82[ASN][1000 genomes]
rs1812122	0.80[ASN][1000 genomes]
rs1993370	0.85[EUR][1000 genomes]
rs2044410	0.85[EUR][1000 genomes]
rs2061162	0.85[EUR][1000 genomes]
rs2084115	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2084116	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2084118	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2100033	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2166361	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2314936	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2314937	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34496480	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3733794	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3932895	0.80[ASN][1000 genomes]
rs3968877	0.80[ASN][1000 genomes]
rs4425487	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5020673	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55870102	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56068548	0.84[EUR][1000 genomes]
rs56202905	0.88[EUR][1000 genomes]
rs56276104	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56365996	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58367004	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59110717	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60663580	0.89[EUR][1000 genomes]
rs61093699	0.82[ASN][1000 genomes]
rs62366375	0.80[ASN][1000 genomes]
rs62366376	0.80[ASN][1000 genomes]
rs62366406	0.82[ASN][1000 genomes]
rs62366414	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62366417	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62366423	0.89[EUR][1000 genomes]
rs62366424	0.88[EUR][1000 genomes]
rs62366426	0.88[EUR][1000 genomes]
rs62366455	0.85[EUR][1000 genomes]
rs62366458	0.85[EUR][1000 genomes]
rs62367762	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62367766	0.85[EUR][1000 genomes]
rs6453075	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6453077	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6453084	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6453086	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6453087	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6859014	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6861730	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6863738	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6866082	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6873067	0.83[EUR][1000 genomes]
rs6874094	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6874609	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6877116	0.88[EUR][1000 genomes]
rs6877442	0.88[EUR][1000 genomes]
rs6879781	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6882499	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6883061	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6884843	0.89[EUR][1000 genomes]
rs6885093	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6885675	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6890815	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6897698	0.88[EUR][1000 genomes]
rs6897904	0.88[EUR][1000 genomes]
rs72764666	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73120619	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7708203	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7724292	0.82[EUR][1000 genomes]
rs7728889	0.85[EUR][1000 genomes]
rs820826	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9686657	0.90[EUR][1000 genomes];0.81[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	nsv598653	chr5:73992881-74095542	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs62366408	NSA2	cis	Nerve Tibial	GTEx
rs62366408	NSA2	cis	Esophagus Mucosa	GTEx
rs62366408	NSA2	cis	Adipose Subcutaneous	GTEx
rs62366408	NSA2	cis	lung	GTEx
rs62366408	NSA2	cis	Muscle Skeletal	GTEx
rs62366408	NSA2	cis	Esophagus Muscularis	GTEx
rs62366408	NSA2	cis	Skin Sun Exposed Lower leg	GTEx
rs62366408	NSA2	cis	Thyroid	GTEx
rs62366408	NSA2	cis	Artery Tibial	GTEx
rs62366408	TINP1	Cis_1M	lymphoblastoid	RTeQTL
rs62366408	NSA2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:73982000-74061800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:73999800-74060800	Weak transcription	Pancreas	Pancrea
3	chr5:73999800-74062200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:74002600-74061800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:74008400-74060200	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr5:74008400-74060200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr5:74010400-74059600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr5:74018000-74060800	Weak transcription	Gastric	stomach
9	chr5:74018600-74062000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr5:74019200-74058600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:74021600-74060800	Weak transcription	Spleen	Spleen
12	chr5:74022000-74060800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:74025000-74062000	Weak transcription	Aorta	Aorta
14	chr5:74032000-74054200	Weak transcription	Lung	lung
15	chr5:74040000-74054200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr5:74043200-74054200	Weak transcription	Colonic Mucosa	Colon
17	chr5:74044400-74061000	Weak transcription	Fetal Heart	heart
18	chr5:74044400-74061000	Weak transcription	Right Ventricle	heart
19	chr5:74045000-74059600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr5:74045200-74061800	Weak transcription	Esophagus	oesophagus
21	chr5:74045800-74058800	Strong transcription	Primary T cells from cord blood	blood
22	chr5:74047000-74054200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr5:74047200-74054200	Weak transcription	HepG2	liver
24	chr5:74047400-74053800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr5:74047400-74054000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr5:74047400-74054200	Weak transcription	Left Ventricle	heart
27	chr5:74047400-74061800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr5:74047800-74054200	Weak transcription	NHEK	skin
29	chr5:74048600-74055600	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr5:74049000-74054600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr5:74049000-74056200	Weak transcription	Stomach Mucosa	stomach
32	chr5:74049400-74054200	Weak transcription	Brain Angular Gyrus	brain
33	chr5:74050000-74056600	Strong transcription	HSMM	muscle
34	chr5:74050400-74058000	Strong transcription	Fetal Intestine Large	intestine
35	chr5:74050800-74054600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr5:74050800-74055400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:74050800-74059200	Strong transcription	Fetal Thymus	thymus
38	chr5:74051000-74056400	Strong transcription	HMEC	breast
39	chr5:74051000-74056800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:74051000-74059600	Strong transcription	Primary B cells from cord blood	blood
41	chr5:74051200-74060000	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr5:74051400-74054000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr5:74051400-74054800	Strong transcription	Fetal Kidney	kidney
44	chr5:74051400-74055400	Strong transcription	Duodenum Mucosa	Duodenum
45	chr5:74051400-74058400	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr5:74051400-74059800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr5:74051400-74060200	Strong transcription	Liver	Liver
48	chr5:74051400-74061200	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr5:74051600-74054600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr5:74051600-74054800	Strong transcription	Brain Anterior Caudate	brain

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