Variant report

Variant	rs72764656
Chromosome Location	chr5:74061281-74061282
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:74061136-74061420	HepG2	liver:	n/a	n/a
2	TBP	chr5:74061095-74061289	HepG2	liver:	n/a	n/a
3	POLR2A	chr5:74061213-74061417	HepG2	liver:	n/a	n/a
4	POLR2A	chr5:74061055-74061331	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
NSA2	TF binding region

Extended variants
information (count: 85 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1048167	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10515192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515199	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11739122	0.88[AFR][1000 genomes]
rs11742773	0.92[AFR][1000 genomes]
rs11749137	0.86[AFR][1000 genomes]
rs11959570	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1350097	0.89[AFR][1000 genomes]
rs16872220	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872231	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872235	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872242	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872259	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872323	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872345	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872347	0.81[AFR][1000 genomes]
rs16872349	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872362	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17561738	0.86[ASN][1000 genomes]
rs2084116	0.92[AFR][1000 genomes]
rs2084118	0.92[AFR][1000 genomes]
rs2100033	0.92[AFR][1000 genomes]
rs3733794	0.94[AFR][1000 genomes]
rs55899032	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55920995	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56127814	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56192858	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56203772	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57202395	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57549677	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58864890	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60492282	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60663580	0.93[AFR][1000 genomes]
rs62366414	0.93[AFR][1000 genomes]
rs62366423	0.86[AFR][1000 genomes]
rs62366426	0.86[AFR][1000 genomes]
rs6453076	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453079	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453082	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6861935	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6870806	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6873912	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873998	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6877188	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6877442	0.86[AFR][1000 genomes]
rs6881400	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6882035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6882499	0.87[AFR][1000 genomes]
rs6883061	0.92[AFR][1000 genomes]
rs6883278	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6883420	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6884338	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884843	0.86[AFR][1000 genomes]
rs6885675	0.92[AFR][1000 genomes]
rs6894177	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6897698	0.86[AFR][1000 genomes]
rs6897904	0.86[AFR][1000 genomes]
rs6898684	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764630	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764643	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764647	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764648	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764650	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764655	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764657	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764663	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764669	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764675	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764676	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764683	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764684	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764687	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764690	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72766504	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7705519	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7713812	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728889	0.81[AFR][1000 genomes]
rs7732440	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7732843	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957680	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9686657	0.92[AFR][1000 genomes]
rs9765469	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs72764656	NSA2	cis	Skin Sun Exposed Lower leg	GTEx
rs72764656	NSA2	cis	Esophagus Mucosa	GTEx
rs72764656	NSA2	cis	Stomach	GTEx
rs72764656	NSA2	cis	lung	GTEx
rs72764656	NSA2	cis	Muscle Skeletal	GTEx
rs72764656	NSA2	cis	Esophagus Muscularis	GTEx
rs72764656	NSA2	cis	Artery Tibial	GTEx
rs72764656	NSA2	cis	Nerve Tibial	GTEx
rs72764656	NSA2	cis	Whole Blood	GTEx
rs72764656	NSA2	cis	Thyroid	GTEx
rs72764656	NSA2	cis	Heart Left Ventricle	GTEx
rs72764656	NSA2	cis	Adipose Subcutaneous	GTEx
rs72764656	NSA2	cis	Artery Aorta	GTEx

Chromatin state (count:127 , 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	chr5:73999800-74062200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:74002600-74061800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:74018600-74062000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:74025000-74062000	Weak transcription	Aorta	Aorta
6	chr5:74045200-74061800	Weak transcription	Esophagus	oesophagus
7	chr5:74047400-74061800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:74052800-74062000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:74055200-74061600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:74056600-74061800	Enhancers	HMEC	breast
11	chr5:74058000-74061400	Weak transcription	Fetal Muscle Leg	muscle
12	chr5:74058200-74061800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr5:74058800-74061400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr5:74059000-74062000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:74059000-74062000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr5:74059200-74061600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr5:74059200-74061800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr5:74059600-74062000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr5:74059800-74061400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr5:74059800-74061800	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr5:74059800-74062000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr5:74060000-74061800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr5:74060200-74061600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:74060200-74061800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr5:74060200-74061800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr5:74060200-74061800	Enhancers	Fetal Intestine Large	intestine
27	chr5:74060200-74062000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr5:74060200-74062000	Enhancers	Small Intestine	intestine
29	chr5:74060200-74062200	Enhancers	Fetal Brain Male	brain
30	chr5:74060400-74061600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:74060600-74061800	Enhancers	Primary T cells fromperipheralblood	blood
32	chr5:74060600-74061800	Enhancers	Left Ventricle	heart
33	chr5:74060600-74061800	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr5:74060600-74062000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr5:74060600-74062000	Enhancers	Ovary	ovary
36	chr5:74060600-74062000	Enhancers	Stomach Mucosa	stomach
37	chr5:74060800-74061400	Transcr. at gene 5' and 3'	HSMM	muscle
38	chr5:74060800-74061600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr5:74060800-74061600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr5:74060800-74061600	Enhancers	Gastric	stomach
41	chr5:74060800-74061800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:74060800-74061800	Enhancers	Liver	Liver
43	chr5:74060800-74061800	Enhancers	Colonic Mucosa	Colon
44	chr5:74060800-74061800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr5:74060800-74061800	Genic enhancers	Fetal Stomach	stomach
46	chr5:74060800-74061800	Enhancers	Fetal Thymus	thymus
47	chr5:74060800-74061800	Enhancers	Pancreas	Pancrea
48	chr5:74060800-74061800	Enhancers	Right Atrium	heart
49	chr5:74060800-74062000	Enhancers	Primary B cells from cord blood	blood
50	chr5:74060800-74062000	Enhancers	Primary T helper naive cells from peripheral blood	blood

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