Variant report

Variant	rs11564405
Chromosome Location	chr18:25658066-25658067
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10502507	0.88[CEU][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1078501	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10853680	0.81[CEU][hapmap];0.90[EUR][1000 genomes]
rs10853681	0.87[CEU][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11083245	0.85[CEU][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11083246	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083248	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11564297	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11564308	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs11564316	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11564329	0.88[CEU][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11564330	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs11564332	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs11564393	0.86[CEU][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11564396	0.81[CEU][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11564397	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11564400	0.82[CEU][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11564409	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11564412	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs11564413	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs11873053	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12958882	0.90[EUR][1000 genomes]
rs1373136	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1373138	0.82[CEU][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1443450	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs1443451	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs1443453	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs17445875	0.90[EUR][1000 genomes]
rs17446001	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs17446316	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17462962	0.86[EUR][1000 genomes]
rs17463213	0.88[CEU][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17463233	0.88[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17463295	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17468531	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17468636	0.86[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17468678	1.00[CEU][hapmap]
rs1808940	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1816825	0.81[CEU][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1838161	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs1867285	0.87[CEU][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1941180	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs1944292	0.88[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1944294	0.81[CEU][hapmap];0.90[EUR][1000 genomes]
rs1972934	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2053599	0.88[CEU][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2156605	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs2218361	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs2310784	0.90[EUR][1000 genomes]
rs4144654	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs4598992	0.81[CEU][hapmap];0.90[EUR][1000 genomes]
rs4800837	0.84[EUR][1000 genomes]
rs4800838	0.91[EUR][1000 genomes]
rs4800839	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs4800840	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4800841	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7230771	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7237382	0.82[CEU][hapmap]
rs72639459	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8091314	0.82[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8091763	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs8092004	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs874314	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs894679	1.00[CEU][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9635986	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9789154	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9789221	0.87[CEU][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[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

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:25645000-25658200	Weak transcription	Fetal Brain Female	brain
2	chr18:25646200-25666400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr18:25649600-25661400	Enhancers	Fetal Heart	heart
4	chr18:25650600-25666800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr18:25651200-25661800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr18:25651600-25665200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr18:25652400-25659600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr18:25652400-25659600	Weak transcription	Right Atrium	heart
9	chr18:25652600-25659600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr18:25652600-25661800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr18:25652600-25663800	Weak transcription	Right Ventricle	heart
12	chr18:25654000-25666000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr18:25654400-25660000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr18:25655600-25659600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr18:25655600-25660800	Weak transcription	Left Ventricle	heart
16	chr18:25655800-25659800	Weak transcription	Brain Germinal Matrix	brain
17	chr18:25655800-25660800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr18:25655800-25690800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr18:25656000-25658200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr18:25656000-25659600	Weak transcription	HSMM	muscle
21	chr18:25656200-25658200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr18:25656200-25658200	Weak transcription	HSMMtube	muscle
23	chr18:25656200-25658400	Weak transcription	HepG2	liver
24	chr18:25656200-25663000	Weak transcription	Brain Angular Gyrus	brain
25	chr18:25656200-25663000	Weak transcription	Brain Anterior Caudate	brain
26	chr18:25656400-25658200	Weak transcription	Osteobl	bone
27	chr18:25656400-25662600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr18:25656800-25658600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr18:25657200-25658200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr18:25657200-25663800	Weak transcription	Brain Hippocampus Middle	brain
31	chr18:25657200-25666800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr18:25657400-25658400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr18:25657400-25658400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr18:25657400-25658400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr18:25657400-25658600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr18:25657400-25658800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr18:25657400-25659000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr18:25657400-25659000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr18:25657400-25663200	Weak transcription	Brain Substantia Nigra	brain
40	chr18:25657600-25658800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr18:25657600-25660200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr18:25657800-25658200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr18:25657800-25666000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr18:25658000-25659000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr18:25658000-25659000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr18:25658000-25659200	Flanking Active TSS	A549	lung
47	chr18:25658000-25660400	Enhancers	NH-A	brain

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