Variant report

Variant	rs62368566
Chromosome Location	chr5:43672081-43672082
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10042852	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10068765	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10074229	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10077102	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10155531	0.83[AFR][1000 genomes]
rs10461744	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11737988	0.82[AFR][1000 genomes]
rs13161838	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13356232	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16873432	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16873435	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16873438	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34361740	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3792918	0.81[EUR][1000 genomes]
rs3805722	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62367650	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62368560	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62368565	0.97[ASN][1000 genomes]
rs62368568	0.85[ASN][1000 genomes]
rs62368594	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6451720	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6863699	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6872959	0.83[AFR][1000 genomes]
rs6875118	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6893250	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6896932	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6898436	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71629185	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7713458	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7713749	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7737947	0.81[EUR][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	nsv881017	chr5:43444826-43731692	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
2	nsv881108	chr5:43527432-43800333	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv968171	chr5:43665149-43674339	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv3471542	chr5:43665651-43824536	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	esv3471543	chr5:43665767-43824443	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62368566	NNT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43650200-43685400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr5:43650600-43673000	Weak transcription	Right Ventricle	heart
3	chr5:43650800-43673200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:43650800-43676200	Weak transcription	Brain Anterior Caudate	brain
5	chr5:43653000-43675600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr5:43653400-43674200	Weak transcription	HSMMtube	muscle
7	chr5:43657000-43674400	Weak transcription	Pancreas	Pancrea
8	chr5:43657600-43676200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr5:43657600-43695200	Weak transcription	K562	blood
10	chr5:43659400-43696800	Weak transcription	Gastric	stomach
11	chr5:43659600-43675400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr5:43659600-43678200	Weak transcription	Brain Hippocampus Middle	brain
13	chr5:43659600-43680400	Weak transcription	Psoas Muscle	Psoas
14	chr5:43659600-43706200	Weak transcription	Small Intestine	intestine
15	chr5:43659600-43710000	Weak transcription	Ovary	ovary
16	chr5:43660000-43685600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:43660200-43684800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr5:43661000-43673200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr5:43661000-43675600	Weak transcription	Primary T cells from cord blood	blood
20	chr5:43661000-43675600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr5:43661000-43675600	Weak transcription	Fetal Kidney	kidney
22	chr5:43661000-43675600	Weak transcription	Left Ventricle	heart
23	chr5:43661000-43676200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr5:43661000-43677000	Weak transcription	Brain Angular Gyrus	brain
25	chr5:43661000-43677000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr5:43661000-43680400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr5:43661000-43680400	Weak transcription	Brain Substantia Nigra	brain
28	chr5:43661000-43680400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr5:43661000-43680400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr5:43661000-43680400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr5:43661000-43680600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr5:43661000-43682400	Weak transcription	Fetal Muscle Leg	muscle
33	chr5:43661000-43682600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr5:43661000-43683200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr5:43661000-43695600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr5:43661000-43702800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr5:43661000-43711400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr5:43661200-43678400	Weak transcription	HUVEC	blood vessel
39	chr5:43661600-43675600	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr5:43662400-43675400	Weak transcription	Hela-S3	cervix
41	chr5:43664000-43674200	Weak transcription	Primary B cells from cord blood	blood
42	chr5:43664000-43676200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr5:43664600-43675800	Weak transcription	Liver	Liver
44	chr5:43664800-43672600	Weak transcription	Adipose Nuclei	Adipose
45	chr5:43664800-43699800	Weak transcription	Colon Smooth Muscle	Colon
46	chr5:43665200-43674200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr5:43665200-43674200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr5:43665200-43674200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr5:43665200-43674400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr5:43665200-43675600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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