Variant report

Variant	rs28478451
Chromosome Location	chr3:81627864-81627865
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11920137	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11920270	0.82[ASN][1000 genomes]
rs11922101	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13319440	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1461607	0.89[ASN][1000 genomes]
rs1984974	0.91[ASN][1000 genomes]
rs2009766	0.96[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2228389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291593	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28415702	0.96[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28702560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28780766	0.96[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3821555	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55828412	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56037559	0.83[AMR][1000 genomes]
rs57135543	0.83[AMR][1000 genomes]
rs58339236	0.82[ASN][1000 genomes]
rs58977050	0.89[ASN][1000 genomes]
rs59161789	0.80[ASN][1000 genomes]
rs60844651	0.80[ASN][1000 genomes]
rs6762839	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72904318	0.89[ASN][1000 genomes]
rs72904375	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72904388	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72904392	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72904402	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7617859	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7619190	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7629051	0.96[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9309873	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9810626	0.83[AMR][1000 genomes]
rs9813324	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9815184	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9820089	0.91[ASN][1000 genomes]
rs9822535	0.96[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9825828	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9828209	0.80[ASN][1000 genomes]
rs9828883	0.96[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9842657	0.96[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9848657	0.80[ASN][1000 genomes]
rs9854820	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9865935	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9868543	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9876575	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[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	nsv934018	chr3:81413060-81655338	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv933756	chr3:81413060-81754738	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1003217	chr3:81435044-81752521	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1012133	chr3:81499082-81817471	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv933259	chr3:81523854-81730617	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv949545	chr3:81523898-81893929	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv999587	chr3:81534364-81707800	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv536603	chr3:81534364-81707800	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81581600-81628200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:81584200-81636600	Weak transcription	Placenta	Placenta
3	chr3:81603600-81726400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:81604200-81641200	Weak transcription	HSMMtube	muscle
5	chr3:81608600-81644000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:81609200-81636600	Weak transcription	Pancreas	Pancrea
7	chr3:81609400-81635200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:81611600-81628600	Weak transcription	Spleen	Spleen
9	chr3:81611600-81629000	Weak transcription	NHLF	lung
10	chr3:81612000-81630400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:81612800-81631000	Weak transcription	Fetal Kidney	kidney
12	chr3:81613600-81699200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:81614000-81629600	Weak transcription	Psoas Muscle	Psoas
14	chr3:81614000-81638200	Weak transcription	Lung	lung
15	chr3:81614000-81693600	Weak transcription	Aorta	Aorta
16	chr3:81614200-81628800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:81614200-81640400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:81614400-81629600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:81614400-81643600	Weak transcription	Primary T cells from cord blood	blood
20	chr3:81614400-81688800	Weak transcription	Right Ventricle	heart
21	chr3:81614600-81633400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:81614600-81634200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:81617600-81631200	Weak transcription	Gastric	stomach
24	chr3:81618800-81629600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:81621800-81629000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:81622000-81633000	Weak transcription	Hela-S3	cervix
27	chr3:81622200-81632600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:81622400-81641600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:81622600-81629600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:81622600-81644600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:81622800-81643000	Weak transcription	Small Intestine	intestine
32	chr3:81623200-81641600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:81623600-81629600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:81623800-81641600	Weak transcription	GM12878-XiMat	blood
35	chr3:81624200-81641200	Weak transcription	NH-A	brain
36	chr3:81624600-81644400	Weak transcription	Esophagus	oesophagus
37	chr3:81624800-81639600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr3:81625000-81633400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:81625200-81639400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr3:81625200-81643400	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr3:81625600-81631400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr3:81625600-81637800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:81625600-81639600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr3:81625600-81644000	Strong transcription	Dnd41	blood
45	chr3:81625800-81629000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr3:81626200-81671000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:81626400-81641400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:81626400-81671800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:81626600-81629600	Weak transcription	Ovary	ovary
50	chr3:81626600-81639600	Weak transcription	Left Ventricle	heart

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