Variant report

Variant	rs623234
Chromosome Location	chr18:25589391-25589392
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10502507	0.82[CHB][hapmap]
rs1078501	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs10853680	0.82[CHB][hapmap]
rs10853681	0.82[CHB][hapmap]
rs1122356	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1148376	0.84[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs11564297	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs11564316	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs11564330	0.82[CHB][hapmap]
rs11564332	0.82[CHB][hapmap]
rs11564396	0.88[CHB][hapmap];0.86[CHD][hapmap]
rs11564400	0.94[CHB][hapmap]
rs11564409	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs11564412	0.82[CHB][hapmap]
rs11564413	0.82[CHB][hapmap]
rs11873053	0.94[CHB][hapmap]
rs1220015	0.85[CEU][hapmap];0.88[CHB][hapmap]
rs1220016	0.85[CEU][hapmap];0.88[CHB][hapmap];0.80[EUR][1000 genomes]
rs1220019	0.85[CEU][hapmap]
rs1220146	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1228419	0.85[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap]
rs1234682	0.85[CEU][hapmap];0.94[CHB][hapmap]
rs1238755	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1373136	0.94[CHB][hapmap]
rs1373138	0.88[CHB][hapmap]
rs1443450	0.82[CHB][hapmap]
rs1443453	0.82[CHB][hapmap]
rs17446001	0.82[CHB][hapmap]
rs17463233	0.82[CHB][hapmap]
rs17468531	0.94[CHB][hapmap]
rs17468636	0.82[CHB][hapmap]
rs1816825	1.00[CHB][hapmap];0.89[CHD][hapmap]
rs1867285	0.82[CHB][hapmap]
rs1941180	0.80[CHB][hapmap]
rs1972934	0.82[CHB][hapmap]
rs2053599	0.82[CHB][hapmap]
rs2218361	0.82[CHB][hapmap]
rs2920447	0.85[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap]
rs4598992	0.82[CHB][hapmap]
rs4800838	0.82[CHB][hapmap]
rs4800840	1.00[CHB][hapmap]
rs4800841	0.82[CHB][hapmap]
rs490820	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs500643	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs533602	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs539075	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs565509	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs568575	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs576467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs584936	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs587526	0.85[CEU][hapmap];0.88[CHB][hapmap];0.80[EUR][1000 genomes]
rs587613	0.85[CEU][hapmap];0.94[CHB][hapmap]
rs597591	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs602819	0.85[CEU][hapmap];0.94[CHB][hapmap];0.81[EUR][1000 genomes]
rs610906	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs614966	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs643555	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs647733	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs656642	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs665651	0.85[CEU][hapmap];0.94[CHB][hapmap]
rs665781	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs673008	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs683457	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs694943	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs7230771	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs7237382	0.88[CHB][hapmap]
rs8087457	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8087860	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs8091314	0.88[CHB][hapmap]
rs8091763	0.82[CHB][hapmap]
rs8092004	0.82[CHB][hapmap]
rs9635986	0.87[CHB][hapmap]
rs9789154	1.00[CHB][hapmap]
rs9789221	0.82[CHB][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs623234	RIOK3	cis	parietal	SCAN

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	chr18:25572800-25589800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr18:25573000-25590000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr18:25573600-25591200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr18:25573600-25593400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr18:25575600-25591400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr18:25577000-25591000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr18:25577600-25589800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr18:25578200-25591400	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr18:25579200-25591400	Weak transcription	HepG2	liver
17	chr18:25580600-25593400	Weak transcription	Ovary	ovary
18	chr18:25580600-25595800	Weak transcription	Left Ventricle	heart
19	chr18:25580800-25589600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr18:25582400-25593200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr18:25582600-25594000	Weak transcription	Dnd41	blood
22	chr18:25583600-25599000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr18:25583800-25593600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr18:25583800-25621400	Weak transcription	Right Ventricle	heart
25	chr18:25584200-25592400	Weak transcription	Brain Angular Gyrus	brain
26	chr18:25584400-25594200	Weak transcription	Brain Anterior Caudate	brain
27	chr18:25584400-25595000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr18:25585200-25592800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr18:25585400-25593400	Weak transcription	Fetal Brain Male	brain
30	chr18:25585600-25591400	Weak transcription	Fetal Lung	lung
31	chr18:25585600-25592400	Weak transcription	Brain Hippocampus Middle	brain
32	chr18:25585600-25593400	Weak transcription	HSMMtube	muscle
33	chr18:25585800-25591200	Weak transcription	HSMM	muscle
34	chr18:25585800-25594000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr18:25586000-25589600	Weak transcription	Fetal Brain Female	brain
36	chr18:25586200-25589600	Weak transcription	Fetal Heart	heart
37	chr18:25586200-25591400	Weak transcription	Brain Germinal Matrix	brain
38	chr18:25587600-25589800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr18:25587600-25592400	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr18:25588000-25590600	Strong transcription	Liver	Liver
41	chr18:25588000-25592600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr18:25588000-25593600	Strong transcription	NH-A	brain
43	chr18:25588200-25591200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr18:25588200-25593400	Weak transcription	HUVEC	blood vessel
45	chr18:25588400-25589400	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr18:25588400-25590000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr18:25588800-25589800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr18:25588800-25591200	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr18:25589200-25591800	Strong transcription	Osteobl	bone

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