Variant report

Variant	rs1139490
Chromosome Location	chr4:100045141-100045142
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 138 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10017466	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1042364	0.86[EUR][1000 genomes]
rs1042365	0.86[EUR][1000 genomes]
rs1126670	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1126671	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1126672	0.85[EUR][1000 genomes]
rs1126673	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1230154	0.82[AMR][1000 genomes]
rs1230156	0.82[AMR][1000 genomes]
rs13102874	0.85[EUR][1000 genomes]
rs13110176	0.85[EUR][1000 genomes]
rs13110764	0.85[EUR][1000 genomes]
rs13112176	0.85[EUR][1000 genomes]
rs13112733	0.85[EUR][1000 genomes]
rs13113166	0.85[EUR][1000 genomes]
rs13127153	0.85[EUR][1000 genomes]
rs13127582	0.85[EUR][1000 genomes]
rs13129488	0.85[EUR][1000 genomes]
rs13132776	0.82[EUR][1000 genomes]
rs13132999	0.84[EUR][1000 genomes]
rs13133633	0.84[EUR][1000 genomes]
rs13133647	0.85[EUR][1000 genomes]
rs13138294	0.85[EUR][1000 genomes]
rs13140423	0.85[EUR][1000 genomes]
rs13143133	0.85[EUR][1000 genomes]
rs17217949	0.85[EUR][1000 genomes]
rs17218003	0.85[EUR][1000 genomes]
rs17218073	0.85[EUR][1000 genomes]
rs17218108	0.85[EUR][1000 genomes]
rs17218141	0.85[EUR][1000 genomes]
rs17218162	0.85[EUR][1000 genomes]
rs17218239	0.85[EUR][1000 genomes]
rs17218288	0.85[EUR][1000 genomes]
rs17218560	0.85[EUR][1000 genomes]
rs17218602	0.85[EUR][1000 genomes]
rs17817359	0.85[EUR][1000 genomes]
rs17817868	0.85[EUR][1000 genomes]
rs17817958	0.85[EUR][1000 genomes]
rs1984362	0.84[EUR][1000 genomes]
rs1984364	0.83[EUR][1000 genomes]
rs2213035	0.84[EUR][1000 genomes]
rs2602881	0.80[EUR][1000 genomes]
rs2602883	0.80[EUR][1000 genomes]
rs2602888	0.81[EUR][1000 genomes]
rs2602891	0.85[EUR][1000 genomes]
rs2602893	0.86[EUR][1000 genomes]
rs2602894	0.86[EUR][1000 genomes]
rs2602895	0.85[EUR][1000 genomes]
rs2602896	0.86[EUR][1000 genomes]
rs2602897	0.86[EUR][1000 genomes]
rs2851246	0.86[EUR][1000 genomes]
rs2851247	0.86[EUR][1000 genomes]
rs2851248	0.86[EUR][1000 genomes]
rs2851249	0.86[EUR][1000 genomes]
rs2851252	0.85[EUR][1000 genomes]
rs2851253	0.85[EUR][1000 genomes]
rs2851255	0.82[EUR][1000 genomes]
rs2851270	0.82[AMR][1000 genomes]
rs28987088	0.85[EUR][1000 genomes]
rs28987097	0.85[EUR][1000 genomes]
rs28987098	0.85[EUR][1000 genomes]
rs28987100	0.85[EUR][1000 genomes]
rs28987101	0.84[EUR][1000 genomes]
rs28987102	0.85[EUR][1000 genomes]
rs29001183	0.85[EUR][1000 genomes]
rs29001194	0.85[EUR][1000 genomes]
rs29001195	0.85[EUR][1000 genomes]
rs29001196	0.85[EUR][1000 genomes]
rs29001199	0.85[EUR][1000 genomes]
rs29001201	0.85[EUR][1000 genomes]
rs29001202	0.84[EUR][1000 genomes]
rs29001203	0.85[EUR][1000 genomes]
rs29001208	0.85[EUR][1000 genomes]
rs29001209	0.85[EUR][1000 genomes]
rs29001211	0.85[EUR][1000 genomes]
rs29001212	0.85[EUR][1000 genomes]
rs29001214	0.85[EUR][1000 genomes]
rs29001215	0.85[EUR][1000 genomes]
rs29001216	0.85[EUR][1000 genomes]
rs29001223	0.85[EUR][1000 genomes]
rs29001224	0.85[EUR][1000 genomes]
rs29001229	0.86[EUR][1000 genomes]
rs29001231	0.86[EUR][1000 genomes]
rs29001232	0.86[EUR][1000 genomes]
rs2924583	0.86[EUR][1000 genomes]
rs34071486	0.85[EUR][1000 genomes]
rs34118841	0.82[EUR][1000 genomes]
rs34360292	0.85[EUR][1000 genomes]
rs34634551	0.84[EUR][1000 genomes]
rs34805407	0.85[EUR][1000 genomes]
rs34876213	0.85[EUR][1000 genomes]
rs34936974	0.85[EUR][1000 genomes]
rs35062722	0.83[EUR][1000 genomes]
rs35073321	0.85[EUR][1000 genomes]
rs35146617	0.83[EUR][1000 genomes]
rs35361391	0.84[EUR][1000 genomes]
rs35491981	0.84[EUR][1000 genomes]
rs35662508	0.85[EUR][1000 genomes]
rs35784540	0.85[EUR][1000 genomes]
rs35797419	0.84[EUR][1000 genomes]
rs35988291	0.85[EUR][1000 genomes]
rs36034266	0.85[EUR][1000 genomes]
rs3919370	0.85[EUR][1000 genomes]
rs4699710	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4699712	0.84[EUR][1000 genomes]
rs4699713	0.85[EUR][1000 genomes]
rs4699714	0.85[EUR][1000 genomes]
rs4699716	0.84[EUR][1000 genomes]
rs4699717	0.83[EUR][1000 genomes]
rs4699718	0.84[EUR][1000 genomes]
rs56222233	0.84[EUR][1000 genomes]
rs56272995	0.85[EUR][1000 genomes]
rs56295995	0.85[EUR][1000 genomes]
rs6532795	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6532796	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6532798	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67311928	0.85[EUR][1000 genomes]
rs6813415	0.85[EUR][1000 genomes]
rs6822348	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6831352	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6837685	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6848050	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7434491	0.84[EUR][1000 genomes]
rs7669636	0.85[EUR][1000 genomes]
rs7670060	0.85[EUR][1000 genomes]
rs7670241	0.84[EUR][1000 genomes]
rs7670638	0.85[EUR][1000 genomes]
rs7672728	0.85[EUR][1000 genomes]
rs7689753	0.85[EUR][1000 genomes]
rs7694646	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1005446	chr4:99988287-100121669	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv537196	chr4:99988287-100121669	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1002574	chr4:100023999-100133693	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3528915	chr4:100025155-100096234	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3528916	chr4:100025155-100096234	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1139490	ADH5	cis	Whole Blood	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100012800-100063800	Weak transcription	Aorta	Aorta
2	chr4:100023000-100055600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:100035000-100098200	Weak transcription	Ovary	ovary
4	chr4:100038800-100055200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:100039800-100064800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:100040000-100050800	Weak transcription	Fetal Intestine Large	intestine
7	chr4:100041000-100046400	Weak transcription	HepG2	liver
8	chr4:100043800-100046200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr4:100044000-100046000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:100044000-100056600	Weak transcription	Fetal Lung	lung
11	chr4:100044400-100063600	Weak transcription	Fetal Intestine Small	intestine
12	chr4:100045000-100045800	Enhancers	Duodenum Mucosa	Duodenum
13	chr4:100045000-100046400	Enhancers	Pancreas	Pancrea
14	chr4:100045000-100048800	Strong transcription	Liver	Liver

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