Variant report

Variant	rs28611062
Chromosome Location	chr3:78986210-78986211
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs13317939	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13322089	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13325291	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1480685	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1480686	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17016573	0.92[EUR][1000 genomes]
rs17016593	0.92[EUR][1000 genomes]
rs2271575	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28431826	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28564735	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28729472	0.80[AFR][1000 genomes]
rs58608513	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59931439	0.92[EUR][1000 genomes]
rs72904273	0.92[EUR][1000 genomes]
rs72904277	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72906141	0.92[EUR][1000 genomes]
rs9631526	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9822620	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9829918	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9835586	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9836486	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9839144	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9839572	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842144	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9861490	0.80[AFR][1000 genomes]
rs9868575	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9871957	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876637	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880690	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv834744	chr3:78911545-79076470	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78959600-78987200	Weak transcription	Fetal Lung	lung
2	chr3:78963200-78991000	Weak transcription	Fetal Brain Male	brain
3	chr3:78967200-78987200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:78967200-79000600	Weak transcription	Fetal Kidney	kidney
5	chr3:78968800-78987200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:78969000-78990800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:78969000-78991000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:78969200-78990400	Weak transcription	NHEK	skin
9	chr3:78969600-79000600	Weak transcription	HepG2	liver
10	chr3:78970400-78991000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:78975600-78987200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:78977200-78990800	Weak transcription	Psoas Muscle	Psoas
13	chr3:78977400-78987200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:78977400-78987200	Weak transcription	Fetal Stomach	stomach
15	chr3:78978400-78992200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:78978800-78990800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:78979600-78987000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:78979600-78987200	Weak transcription	Aorta	Aorta
19	chr3:78980600-78989400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:78981600-78991600	Weak transcription	Fetal Heart	heart
21	chr3:78982400-79001800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:78982800-78987200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:78983800-78989200	Weak transcription	Colon Smooth Muscle	Colon
24	chr3:78984400-78990200	Weak transcription	Osteobl	bone
25	chr3:78985000-78987200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr3:78985200-78989200	Weak transcription	Brain Substantia Nigra	brain
27	chr3:78985400-78987200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:78985600-78987200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:78985800-78987200	Weak transcription	Fetal Muscle Leg	muscle
30	chr3:78985800-78987400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:78985800-78987600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:78985800-78989000	Weak transcription	Placenta	Placenta
33	chr3:78985800-78989800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:78985800-78990400	Weak transcription	NHDF-Ad	bronchial
35	chr3:78986000-78990600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:78986000-78990800	Weak transcription	NHLF	lung
37	chr3:78986200-78987800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr3:78986200-78989000	Weak transcription	Brain Germinal Matrix	brain
39	chr3:78986200-78989800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:78986200-78990800	Weak transcription	Primary T cells from cord blood	blood

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