Variant report

Variant	rs1228419
Chromosome Location	chr18:25665486-25665487
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1078501	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11083248	0.82[CHB][hapmap]
rs1122356	0.88[CHB][hapmap];0.81[CHD][hapmap]
rs1148376	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11564297	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11564316	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11564396	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11564397	0.82[CHB][hapmap]
rs11564400	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11564409	0.94[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs11873053	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1220015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1220016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1220019	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1220146	0.85[CEU][hapmap]
rs1234682	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1373136	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1373138	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17446316	0.93[ASN][1000 genomes]
rs17463295	0.82[CHB][hapmap]
rs17468531	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1816825	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2920447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4800840	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs490820	0.88[CHB][hapmap]
rs500643	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs533602	0.94[CHB][hapmap]
rs539075	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs565509	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs568575	0.94[CHB][hapmap]
rs576467	0.85[CEU][hapmap];0.88[CHB][hapmap]
rs584936	0.88[CHB][hapmap]
rs587526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs587613	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs597591	0.88[CHB][hapmap];0.81[CHD][hapmap]
rs602819	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs610906	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs614966	0.88[CHB][hapmap];0.81[CHD][hapmap]
rs623234	0.85[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap]
rs643555	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs647733	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs656642	0.88[CHB][hapmap]
rs665651	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs665781	0.81[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap]
rs673008	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs683457	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs694943	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7230771	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7237382	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8087457	0.85[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs8087860	0.94[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs8091314	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9635986	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9789154	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1228419	RIOK3	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:25646200-25666400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr18:25650600-25666800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr18:25654000-25666000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr18:25655800-25690800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr18:25657200-25666800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr18:25657800-25666000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr18:25658600-25666800	Weak transcription	Fetal Kidney	kidney
8	chr18:25658800-25666600	Weak transcription	HSMMtube	muscle
9	chr18:25659000-25665600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr18:25660200-25666200	Weak transcription	Osteobl	bone
11	chr18:25660200-25666600	Weak transcription	HSMM	muscle
12	chr18:25660200-25666800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr18:25660200-25666800	Weak transcription	Fetal Brain Male	brain
14	chr18:25661000-25666200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr18:25661200-25666800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr18:25661400-25666400	Weak transcription	HepG2	liver
17	chr18:25662000-25667000	Weak transcription	NHLF	lung
18	chr18:25662600-25667000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr18:25662800-25666400	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr18:25662800-25666600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr18:25662800-25667400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr18:25662800-25668000	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr18:25662800-25670000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr18:25663000-25666200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr18:25663000-25666400	Enhancers	Brain Angular Gyrus	brain
26	chr18:25663000-25667000	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr18:25663200-25666200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr18:25663600-25666400	Enhancers	Brain Anterior Caudate	brain
29	chr18:25663600-25667000	Enhancers	Brain Germinal Matrix	brain
30	chr18:25663800-25666400	Enhancers	Brain Hippocampus Middle	brain
31	chr18:25663800-25667000	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr18:25664000-25667000	Enhancers	Fetal Heart	heart
33	chr18:25664200-25666200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr18:25664200-25667000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr18:25664400-25665800	Enhancers	Right Ventricle	heart
36	chr18:25664400-25666600	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr18:25664600-25665600	Enhancers	Left Ventricle	heart
38	chr18:25664600-25665600	Enhancers	Right Atrium	heart
39	chr18:25664600-25667000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr18:25664800-25665600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr18:25665200-25665600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr18:25665200-25666200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr18:25665200-25666800	Enhancers	NH-A	brain
44	chr18:25665200-25667000	Enhancers	Liver	Liver
45	chr18:25665400-25665600	Enhancers	A549	lung
46	chr18:25665400-25666000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
47	chr18:25665400-25666400	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr18:25665400-25666400	Enhancers	Brain Substantia Nigra	brain

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