Variant report

Variant	rs11564400
Chromosome Location	chr18:25667295-25667296
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10502507	0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1078501	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10853681	0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11083245	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11083246	0.82[CEU][hapmap];0.82[CHB][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11083248	0.82[CEU][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1122356	0.94[CHB][hapmap]
rs1148376	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11564297	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11564316	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11564329	0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11564393	0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs11564396	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564397	0.81[CEU][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11564405	0.82[CEU][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11564409	0.89[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11873053	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1220015	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1220016	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1220019	0.89[ASN][1000 genomes]
rs1228419	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1234682	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1373136	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1373138	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17446316	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17463213	0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17463233	0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17463295	0.82[CEU][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17468531	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17468636	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17468678	0.82[CEU][hapmap]
rs1808940	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1816825	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1867285	0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1944292	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1972934	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2053599	0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2920447	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4800840	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4800841	0.81[CEU][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs490820	0.94[CHB][hapmap]
rs500643	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs533602	0.89[CHB][hapmap]
rs539075	0.93[CHB][hapmap]
rs565509	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs568575	0.88[CHB][hapmap]
rs576467	0.94[CHB][hapmap]
rs584936	0.89[CHB][hapmap]
rs587526	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs587613	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs597591	0.94[CHB][hapmap]
rs602819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs610906	0.93[ASN][1000 genomes]
rs614966	0.94[CHB][hapmap]
rs623234	0.94[CHB][hapmap]
rs643555	0.88[CHB][hapmap]
rs647733	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs656642	0.94[CHB][hapmap]
rs665651	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs665781	0.94[CHB][hapmap]
rs673008	0.94[CHB][hapmap]
rs683457	0.93[ASN][1000 genomes]
rs694943	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7230771	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7237382	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs72639459	0.93[AMR][1000 genomes]
rs8087457	0.81[JPT][hapmap]
rs8087860	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8091314	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs894679	0.81[CEU][hapmap];0.81[CHB][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9635986	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9789154	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9789221	0.89[AMR][1000 genomes];0.84[EUR][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:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:25655800-25690800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr18:25662800-25667400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr18:25662800-25668000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr18:25662800-25670000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr18:25665600-25667600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr18:25665600-25669800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr18:25665600-25671800	Weak transcription	Left Ventricle	heart
8	chr18:25666000-25668000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr18:25666200-25667400	Enhancers	Right Ventricle	heart
10	chr18:25666400-25668000	Enhancers	HUVEC	blood vessel
11	chr18:25666400-25668800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr18:25666400-25671000	Enhancers	HepG2	liver
13	chr18:25666600-25667400	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr18:25666600-25667400	Enhancers	Gastric	stomach
15	chr18:25666600-25667600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
16	chr18:25666600-25667600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr18:25666600-25667600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr18:25666600-25667600	Enhancers	Fetal Lung	lung
19	chr18:25666600-25667800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr18:25666600-25667800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr18:25666600-25668000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr18:25666600-25668000	Enhancers	HSMM	muscle
23	chr18:25666800-25667600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr18:25666800-25667600	Enhancers	Adipose Nuclei	Adipose
25	chr18:25666800-25667600	Enhancers	Aorta	Aorta
26	chr18:25666800-25667600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr18:25666800-25667600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr18:25666800-25667600	Flanking Active TSS	NH-A	brain
29	chr18:25666800-25667800	Enhancers	H9 Cell Line	embryonic stem cell
30	chr18:25666800-25667800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr18:25666800-25667800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr18:25666800-25668600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
33	chr18:25667000-25667400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr18:25667000-25667400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
35	chr18:25667000-25667400	Flanking Active TSS	Liver	Liver
36	chr18:25667000-25667400	Flanking Active TSS	Brain Angular Gyrus	brain
37	chr18:25667000-25667400	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr18:25667000-25667400	Flanking Active TSS	Fetal Brain Male	brain
39	chr18:25667000-25667400	Flanking Active TSS	Fetal Heart	heart
40	chr18:25667000-25667400	Enhancers	Ovary	ovary
41	chr18:25667000-25667400	Flanking Active TSS	A549	lung
42	chr18:25667000-25667600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr18:25667000-25667600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr18:25667000-25667600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr18:25667000-25667600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr18:25667000-25667600	Flanking Active TSS	Brain Anterior Caudate	brain
47	chr18:25667000-25667600	Flanking Active TSS	Brain Cingulate Gyrus	brain
48	chr18:25667000-25667600	Flanking Active TSS	Brain Germinal Matrix	brain
49	chr18:25667000-25667600	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr18:25667000-25667600	Active TSS	Right Atrium	heart

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