Variant report

Variant	rs11564295
Chromosome Location	chr18:25573401-25573402
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11083244	0.86[CEU][hapmap]
rs11083247	0.86[CEU][hapmap]
rs11564298	0.84[ASW][hapmap];0.90[CEU][hapmap];0.85[GIH][hapmap];0.90[LWK][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11564398	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs11564401	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs11564403	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs11564410	0.86[CEU][hapmap];0.89[MEX][hapmap];1.00[YRI][hapmap]
rs11564414	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11564418	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11664205	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11664343	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12956425	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12957780	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12971156	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17468213	0.82[CEU][hapmap]
rs17468261	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17468415	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs17468443	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs17468699	0.86[CEU][hapmap];0.89[YRI][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
rs11564295	RIOK3	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:25531200-25593600	Weak transcription	Fetal Kidney	kidney
2	chr18:25536400-25578200	Weak transcription	Fetal Brain Male	brain
3	chr18:25536800-25574200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr18:25540800-25576400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr18:25542800-25574400	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr18:25545600-25588600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr18:25548800-25574600	Strong transcription	NH-A	brain
8	chr18:25549400-25574000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr18:25553000-25593600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr18:25555600-25574200	Weak transcription	Brain Anterior Caudate	brain
11	chr18:25556200-25574600	Weak transcription	Brain Angular Gyrus	brain
12	chr18:25556200-25586800	Weak transcription	Spleen	Spleen
13	chr18:25556200-25592800	Weak transcription	Aorta	Aorta
14	chr18:25556200-25595800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr18:25556400-25576400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr18:25556400-25584600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr18:25557200-25575000	Weak transcription	Gastric	stomach
18	chr18:25558800-25583600	Weak transcription	Right Ventricle	heart
19	chr18:25559400-25574400	Strong transcription	Liver	Liver
20	chr18:25561800-25574000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr18:25562800-25574000	Strong transcription	HSMM	muscle
22	chr18:25564800-25591400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr18:25565000-25592800	Weak transcription	A549	lung
24	chr18:25565200-25580000	Weak transcription	Ovary	ovary
25	chr18:25565200-25591800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr18:25566400-25584600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr18:25566600-25578400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr18:25567800-25574200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr18:25570800-25574000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr18:25571000-25573600	Strong transcription	Fetal Brain Female	brain
31	chr18:25571000-25573600	Genic enhancers	Fetal Heart	heart
32	chr18:25571400-25574400	Strong transcription	Osteobl	bone
33	chr18:25571600-25573600	Strong transcription	Dnd41	blood
34	chr18:25571600-25573600	Strong transcription	HSMMtube	muscle
35	chr18:25571600-25588800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr18:25571800-25573800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr18:25571800-25574400	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr18:25572000-25573600	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr18:25572000-25574400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr18:25572000-25580600	Weak transcription	Fetal Intestine Large	intestine
41	chr18:25572200-25573600	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr18:25572200-25573800	Strong transcription	Brain Germinal Matrix	brain
43	chr18:25572200-25573800	Weak transcription	Fetal Intestine Small	intestine
44	chr18:25572400-25573600	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr18:25572400-25573600	Strong transcription	Brain Cingulate Gyrus	brain
46	chr18:25572400-25573600	Strong transcription	Brain Hippocampus Middle	brain
47	chr18:25572400-25573600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr18:25572400-25573600	Strong transcription	HepG2	liver
49	chr18:25572400-25573800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr18:25572400-25574000	Strong transcription	Left Ventricle	heart

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