Variant report

Variant	rs17462962
Chromosome Location	chr18:25588694-25588695
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10502506	0.84[ASN][1000 genomes]
rs10502507	0.89[EUR][1000 genomes]
rs10853680	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10853681	0.89[EUR][1000 genomes]
rs11083245	0.88[EUR][1000 genomes]
rs11083246	0.86[EUR][1000 genomes]
rs11083248	0.85[EUR][1000 genomes]
rs11564308	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11564329	0.88[EUR][1000 genomes]
rs11564330	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11564332	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11564397	0.86[EUR][1000 genomes]
rs11564405	0.86[EUR][1000 genomes]
rs11564412	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11564413	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12958882	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1443450	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1443451	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1443453	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17445875	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17446001	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17463213	0.88[EUR][1000 genomes]
rs17463233	0.89[EUR][1000 genomes]
rs17463295	0.85[EUR][1000 genomes]
rs17468636	0.89[EUR][1000 genomes]
rs1808940	0.86[EUR][1000 genomes]
rs1838161	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1867285	0.89[EUR][1000 genomes]
rs1941180	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1944292	0.88[EUR][1000 genomes]
rs1944294	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1972934	0.89[EUR][1000 genomes]
rs2053599	0.88[EUR][1000 genomes]
rs2156605	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2218361	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2310784	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4144654	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4598992	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4800837	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4800838	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4800839	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4800841	0.84[EUR][1000 genomes]
rs490820	0.83[AMR][1000 genomes]
rs568575	0.84[AMR][1000 genomes]
rs673008	0.84[AMR][1000 genomes]
rs72639459	0.84[EUR][1000 genomes]
rs8091763	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8092004	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs874314	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs894679	0.86[EUR][1000 genomes]
rs9789221	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761996	chr18:24866083-25818618	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1066192	chr18:25454413-25606736	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv543669	chr18:25454413-25606736	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv833605	chr18:25467096-25643447	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:25531200-25593600	Weak transcription	Fetal Kidney	kidney
2	chr18:25553000-25593600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr18:25556200-25592800	Weak transcription	Aorta	Aorta
4	chr18:25556200-25595800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr18:25564800-25591400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr18:25565000-25592800	Weak transcription	A549	lung
7	chr18:25565200-25591800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr18:25571600-25588800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr18:25572800-25589800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr18:25573000-25590000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr18:25573600-25591200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr18:25573600-25593400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr18:25575600-25591400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr18:25577000-25591000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr18:25577600-25589800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr18:25578200-25591400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr18:25579200-25591400	Weak transcription	HepG2	liver
18	chr18:25580600-25593400	Weak transcription	Ovary	ovary
19	chr18:25580600-25595800	Weak transcription	Left Ventricle	heart
20	chr18:25580800-25589600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr18:25582400-25593200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr18:25582600-25594000	Weak transcription	Dnd41	blood
23	chr18:25583600-25599000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr18:25583800-25593600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr18:25583800-25621400	Weak transcription	Right Ventricle	heart
26	chr18:25584200-25592400	Weak transcription	Brain Angular Gyrus	brain
27	chr18:25584400-25594200	Weak transcription	Brain Anterior Caudate	brain
28	chr18:25584400-25595000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr18:25585200-25592800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr18:25585400-25593400	Weak transcription	Fetal Brain Male	brain
31	chr18:25585600-25591400	Weak transcription	Fetal Lung	lung
32	chr18:25585600-25592400	Weak transcription	Brain Hippocampus Middle	brain
33	chr18:25585600-25593400	Weak transcription	HSMMtube	muscle
34	chr18:25585800-25591200	Weak transcription	HSMM	muscle
35	chr18:25585800-25594000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr18:25586000-25589600	Weak transcription	Fetal Brain Female	brain
37	chr18:25586200-25589600	Weak transcription	Fetal Heart	heart
38	chr18:25586200-25591400	Weak transcription	Brain Germinal Matrix	brain
39	chr18:25587600-25589800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr18:25587600-25592400	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr18:25588000-25588800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr18:25588000-25590600	Strong transcription	Liver	Liver
43	chr18:25588000-25592600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr18:25588000-25593600	Strong transcription	NH-A	brain
45	chr18:25588200-25591200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr18:25588200-25593400	Weak transcription	HUVEC	blood vessel
47	chr18:25588400-25589200	Weak transcription	Osteobl	bone
48	chr18:25588400-25589400	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr18:25588400-25590000	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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