Variant report

Variant	rs227654
Chromosome Location	chr20:24930801-24930802
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs127131	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182749	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883830	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883831	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064404	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179731	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256031	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227589	0.87[EUR][1000 genomes]
rs227603	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227617	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs227637	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227641	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227642	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227644	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227645	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227647	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227655	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227656	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28815609	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3928737	1.00[ASN][1000 genomes]
rs4239751	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4429533	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4432532	0.88[EUR][1000 genomes]
rs4815358	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815359	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55651048	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55681373	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036998	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037003	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037006	1.00[ASN][1000 genomes]
rs6050123	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050128	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050129	0.84[EUR][1000 genomes]
rs6050199	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050211	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050212	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050214	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050244	1.00[ASN][1000 genomes]
rs6083696	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083697	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083714	0.88[EUR][1000 genomes]
rs6083718	1.00[ASN][1000 genomes]
rs6114995	1.00[ASN][1000 genomes]
rs6138432	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138433	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6515552	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7352631	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761368	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765834	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8121279	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs914312	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv510783	chr20:24889192-24941933	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv524921	chr20:24897355-24932028	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv964444	chr20:24899460-24934649	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv2762068	chr20:24908860-24974986	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24928600-24940400	Weak transcription	Right Atrium	heart
2	chr20:24929400-24931200	Enhancers	Fetal Thymus	thymus
3	chr20:24929400-24932600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
4	chr20:24929400-24933800	Active TSS	Primary B cells from cord blood	blood
5	chr20:24929600-24931000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr20:24929600-24931000	Weak transcription	HSMM	muscle
7	chr20:24929600-24936400	Weak transcription	Fetal Intestine Small	intestine
8	chr20:24929800-24931000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr20:24929800-24931000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
10	chr20:24929800-24931000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr20:24929800-24931200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr20:24929800-24931200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
13	chr20:24929800-24931200	Active TSS	Esophagus	oesophagus
14	chr20:24929800-24931400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr20:24929800-24931400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr20:24929800-24931600	Active TSS	Duodenum Mucosa	Duodenum
17	chr20:24929800-24931800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr20:24929800-24931800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr20:24930000-24931000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
20	chr20:24930000-24931200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr20:24930000-24931200	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr20:24930000-24931400	Active TSS	Adipose Nuclei	Adipose
23	chr20:24930000-24931600	Active TSS	Gastric	stomach
24	chr20:24930000-24933200	Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr20:24930000-24934800	Weak transcription	GM12878-XiMat	blood
26	chr20:24930000-24936400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr20:24930200-24931400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
28	chr20:24930200-24936800	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr20:24930200-24939400	Weak transcription	Right Ventricle	heart
30	chr20:24930400-24931200	Active TSS	Spleen	Spleen
31	chr20:24930400-24932000	Enhancers	HSMMtube	muscle
32	chr20:24930400-24933600	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr20:24930400-24934200	Weak transcription	Pancreas	Pancrea
34	chr20:24930400-24934400	Weak transcription	Lung	lung
35	chr20:24930400-24935000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr20:24930400-24939000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr20:24930600-24931000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr20:24930600-24932600	Weak transcription	Liver	Liver
39	chr20:24930600-24933000	Enhancers	Primary hematopoietic stem cells	blood
40	chr20:24930600-24935600	Weak transcription	Primary T cells from cord blood	blood
41	chr20:24930600-24943000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr20:24930800-24931000	Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr20:24930800-24931000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr20:24930800-24931400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr20:24930800-24931400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr20:24930800-24931400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr20:24930800-24932400	Weak transcription	K562	blood
48	chr20:24930800-24933400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr20:24930800-24933600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr20:24930800-24933800	Enhancers	Placenta	Placenta

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