Variant report

Variant	rs72764657
Chromosome Location	chr5:74064340-74064341
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	MXI1	chr5:74061749-74064458	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr5:74062258-74064596	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:73979647..73982006-chr5:74061742..74064417,2	K562	blood:
2	chr5:73980885..73983030-chr5:74062980..74064496,2	MCF-7	breast:
3	chr5:74062787..74065047-chr5:74073990..74076959,3	MCF-7	breast:
4	chr5:73978938..73982006-chr5:74061565..74064417,3	K562	blood:

Variant related genes	Relation type
GFM2	TF binding region
NSA2	TF binding region
ENSG00000049860	Chromatin interaction
ENSG00000199645	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	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10515192	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515194	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515199	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11739122	0.87[AFR][1000 genomes]
rs11742773	0.91[AFR][1000 genomes]
rs11749137	0.85[AFR][1000 genomes]
rs11959570	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1350097	0.88[AFR][1000 genomes]
rs16872220	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872231	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872235	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872242	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872259	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872323	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872345	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872347	0.80[AFR][1000 genomes]
rs16872349	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872362	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17561738	0.86[ASN][1000 genomes]
rs2084116	0.91[AFR][1000 genomes]
rs2084118	0.91[AFR][1000 genomes]
rs2100033	0.91[AFR][1000 genomes]
rs3733794	0.93[AFR][1000 genomes]
rs55899032	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55920995	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56127814	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56192858	0.84[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	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57549677	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58864890	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60492282	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60663580	0.92[AFR][1000 genomes]
rs62366414	0.92[AFR][1000 genomes]
rs62366423	0.86[AFR][1000 genomes]
rs62366426	0.85[AFR][1000 genomes]
rs6453076	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453079	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453082	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6861935	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6870806	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6873912	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873998	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6877188	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6877442	0.86[AFR][1000 genomes]
rs6881400	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6882035	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6882499	0.86[AFR][1000 genomes]
rs6883061	0.91[AFR][1000 genomes]
rs6883278	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6883420	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6884338	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884843	0.85[AFR][1000 genomes]
rs6885675	0.91[AFR][1000 genomes]
rs6894177	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6897698	0.85[AFR][1000 genomes]
rs6897904	0.85[AFR][1000 genomes]
rs6898684	0.98[AFR][1000 genomes];0.93[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	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764647	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764648	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764650	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764654	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764655	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764656	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764663	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764669	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764675	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764676	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764683	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764684	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764687	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764690	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72766504	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7705519	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7713812	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728889	0.80[AFR][1000 genomes]
rs7732440	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7732843	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957680	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9686657	0.91[AFR][1000 genomes]
rs9765469	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
rs72764657	NSA2	cis	Heart Left Ventricle	GTEx
rs72764657	NSA2	cis	Artery Aorta	GTEx
rs72764657	NSA2	cis	Skin Sun Exposed Lower leg	GTEx
rs72764657	NSA2	cis	Esophagus Muscularis	GTEx
rs72764657	NSA2	cis	Thyroid	GTEx
rs72764657	NSA2	cis	Esophagus Mucosa	GTEx
rs72764657	NSA2	cis	Whole Blood	GTEx
rs72764657	NSA2	cis	lung	GTEx
rs72764657	NSA2	cis	Nerve Tibial	GTEx
rs72764657	NSA2	cis	Artery Tibial	GTEx
rs72764657	NSA2	cis	Stomach	GTEx
rs72764657	NSA2	cis	Adipose Subcutaneous	GTEx
rs72764657	NSA2	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74061000-74064600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:74061200-74064400	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr5:74061400-74064400	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr5:74061800-74064400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr5:74061800-74064600	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr5:74063200-74064400	Active TSS	Right Atrium	heart
7	chr5:74063400-74064400	Flanking Active TSS	Liver	Liver
8	chr5:74063600-74064400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:74063600-74064400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:74063600-74064400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr5:74063600-74064400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr5:74063600-74064400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:74063600-74064400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:74063600-74064400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr5:74063600-74064400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:74063600-74064400	Flanking Active TSS	Brain Germinal Matrix	brain
17	chr5:74063600-74064400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr5:74063600-74064400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr5:74063600-74064400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr5:74063800-74064400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:74063800-74064400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr5:74063800-74064400	Enhancers	Stomach Mucosa	stomach
23	chr5:74063800-74064400	Flanking Active TSS	Dnd41	blood
24	chr5:74063800-74064400	Flanking Active TSS	HMEC	breast
25	chr5:74063800-74064400	Flanking Active TSS	HSMM	muscle
26	chr5:74063800-74064400	Flanking Active TSS	NHEK	skin
27	chr5:74063800-74069200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr5:74064000-74064400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr5:74064000-74064400	Enhancers	Fetal Heart	heart
30	chr5:74064000-74064400	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr5:74064000-74064400	Flanking Active TSS	GM12878-XiMat	blood
32	chr5:74064000-74064400	Flanking Active TSS	HepG2	liver
33	chr5:74064000-74064600	Flanking Active TSS	A549	lung
34	chr5:74064000-74064600	Flanking Active TSS	K562	blood
35	chr5:74064000-74065000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr5:74064000-74065000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr5:74064000-74065800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:74064000-74067800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr5:74064000-74068000	Weak transcription	Ovary	ovary
40	chr5:74064000-74068200	Weak transcription	Lung	lung
41	chr5:74064000-74070200	Weak transcription	Aorta	Aorta
42	chr5:74064000-74071000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr5:74064000-74076000	Weak transcription	Esophagus	oesophagus
44	chr5:74064000-74077200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr5:74064000-74112400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr5:74064200-74064400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:74064200-74064400	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr5:74064200-74064400	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr5:74064200-74064400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr5:74064200-74064400	Enhancers	Primary T cells from cord blood	blood

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