Variant report

Variant	rs72764654
Chromosome Location	chr5:74059708-74059709
allele	C/T
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	JUND	chr5:74059382-74059715	Hela-S3	cervix:	n/a	chr5:74059530-74059541 chr5:74059396-74059403 chr5:74059396-74059404
2	FOS	chr5:74059347-74059712	MCF10A-Er-Src	breast:	n/a	chr5:74059396-74059403 chr5:74059530-74059541 chr5:74059396-74059404
3	JUND	chr5:74059173-74059810	SK-N-SH	brain:	n/a	chr5:74059530-74059541 chr5:74059396-74059403 chr5:74059396-74059404
4	FOS	chr5:74058390-74059712	MCF10A-Er-Src	breast:	n/a	chr5:74059396-74059403 chr5:74058562-74058573 chr5:74059530-74059541 chr5:74059396-74059404 chr5:74058970-74058981
5	FOS	chr5:74059286-74059718	MCF10A-Er-Src	breast:	n/a	chr5:74059396-74059403 chr5:74059530-74059541 chr5:74059396-74059404
6	FOS	chr5:74059352-74059718	MCF10A-Er-Src	breast:	n/a	chr5:74059396-74059403 chr5:74059530-74059541 chr5:74059396-74059404

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:74058294..74061098-chr5:74061736..74064363,2	K562	blood:

Variant related genes	Relation type
NSA2	TF binding region
ENSG00000164347	Chromatin interaction
ENSG00000164346	Chromatin interaction

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]
rs72764655	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764656	1.00[AFR][1000 genomes];1.00[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
rs72764654	NSA2	cis	Esophagus Muscularis	GTEx
rs72764654	NSA2	cis	Artery Tibial	GTEx
rs72764654	NSA2	cis	Nerve Tibial	GTEx
rs72764654	NSA2	cis	Skin Sun Exposed Lower leg	GTEx
rs72764654	NSA2	cis	Stomach	GTEx
rs72764654	NSA2	cis	Artery Aorta	GTEx
rs72764654	NSA2	cis	Esophagus Mucosa	GTEx
rs72764654	NSA2	cis	Muscle Skeletal	GTEx
rs72764654	NSA2	cis	Heart Left Ventricle	GTEx
rs72764654	NSA2	cis	Adipose Subcutaneous	GTEx
rs72764654	NSA2	cis	lung	GTEx
rs72764654	NSA2	cis	Whole Blood	GTEx
rs72764654	NSA2	cis	Thyroid	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	chr5:74018000-74060800	Weak transcription	Gastric	stomach
8	chr5:74018600-74062000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:74021600-74060800	Weak transcription	Spleen	Spleen
10	chr5:74022000-74060800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr5:74025000-74062000	Weak transcription	Aorta	Aorta
12	chr5:74044400-74061000	Weak transcription	Fetal Heart	heart
13	chr5:74044400-74061000	Weak transcription	Right Ventricle	heart
14	chr5:74045200-74061800	Weak transcription	Esophagus	oesophagus
15	chr5:74047400-74061800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr5:74051200-74060000	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr5:74051400-74059800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr5:74051400-74060200	Strong transcription	Liver	Liver
19	chr5:74051400-74061200	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr5:74051600-74060000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr5:74052200-74060400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr5:74052800-74060800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:74052800-74061000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:74052800-74061000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr5:74052800-74061000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr5:74052800-74061200	Weak transcription	Brain Substantia Nigra	brain
27	chr5:74052800-74062000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr5:74053600-74060800	Weak transcription	Fetal Stomach	stomach
29	chr5:74053600-74061000	Weak transcription	Fetal Intestine Small	intestine
30	chr5:74054400-74060200	Weak transcription	Fetal Brain Male	brain
31	chr5:74054400-74060200	Weak transcription	Small Intestine	intestine
32	chr5:74054600-74059800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr5:74054600-74060000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr5:74054600-74060200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr5:74054600-74060200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr5:74054600-74060600	Weak transcription	Lung	lung
37	chr5:74054600-74060800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr5:74054600-74060800	Weak transcription	Colonic Mucosa	Colon
39	chr5:74054600-74060800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr5:74054800-74060600	Weak transcription	Left Ventricle	heart
41	chr5:74054800-74060600	Weak transcription	Ovary	ovary
42	chr5:74054800-74060600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr5:74054800-74060800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr5:74054800-74060800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr5:74054800-74060800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr5:74054800-74061000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr5:74054800-74061000	Weak transcription	Brain Anterior Caudate	brain
48	chr5:74054800-74061000	Weak transcription	Fetal Kidney	kidney
49	chr5:74054800-74061000	Weak transcription	Thymus	Thymus
50	chr5:74055000-74059800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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