Variant report

Variant	rs28539217
Chromosome Location	chr16:48288722-48288723
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs13332870	1.00[AMR][1000 genomes]
rs13335175	1.00[AMR][1000 genomes]
rs13336203	1.00[AMR][1000 genomes]
rs13336441	1.00[AMR][1000 genomes]
rs13336832	1.00[AMR][1000 genomes]
rs13337923	1.00[AMR][1000 genomes]
rs28361908	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28379458	1.00[AMR][1000 genomes]
rs28473019	1.00[AMR][1000 genomes]
rs28599555	1.00[AMR][1000 genomes]
rs28661941	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28848294	1.00[AMR][1000 genomes]
rs9889104	1.00[AMR][1000 genomes]
rs9922477	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9926437	1.00[AMR][1000 genomes]
rs9926749	1.00[AMR][1000 genomes]
rs9927124	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9928527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9929780	1.00[AMR][1000 genomes]
rs9931267	1.00[AMR][1000 genomes]
rs9931866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9932677	1.00[AMR][1000 genomes]
rs9933958	1.00[AMR][1000 genomes]
rs9934175	1.00[AMR][1000 genomes]
rs9934459	1.00[AMR][1000 genomes]
rs9934918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9936494	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9936636	1.00[AMR][1000 genomes]
rs9936892	1.00[AMR][1000 genomes]
rs9938115	1.00[AMR][1000 genomes]
rs9938350	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9938594	1.00[AMR][1000 genomes]
rs9940237	1.00[AMR][1000 genomes]
rs9941354	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059259	chr16:48113396-48304404	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv542916	chr16:48113396-48304404	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1061316	chr16:48264175-48594219	Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv1821072	chr16:48268318-48504364	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48279400-48312600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:48279600-48292200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr16:48279600-48292600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr16:48279600-48293400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr16:48279600-48293400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr16:48279600-48294200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr16:48279600-48297200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr16:48279600-48311200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr16:48279600-48320200	Weak transcription	Spleen	Spleen
10	chr16:48280400-48289000	Weak transcription	HUVEC	blood vessel
11	chr16:48280400-48292800	Weak transcription	NHDF-Ad	bronchial
12	chr16:48280400-48293400	Weak transcription	Colonic Mucosa	Colon
13	chr16:48280400-48293400	Weak transcription	Thymus	Thymus
14	chr16:48280400-48293400	Weak transcription	HSMMtube	muscle
15	chr16:48280400-48295400	Weak transcription	Brain Germinal Matrix	brain
16	chr16:48280400-48296000	Weak transcription	Fetal Brain Male	brain
17	chr16:48280400-48309400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr16:48280800-48292200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr16:48280800-48304000	Weak transcription	Hela-S3	cervix
20	chr16:48281200-48291600	Weak transcription	Fetal Brain Female	brain
21	chr16:48281400-48289000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr16:48281400-48313200	Weak transcription	Right Atrium	heart
23	chr16:48281600-48289000	Weak transcription	Right Ventricle	heart
24	chr16:48281600-48290600	Weak transcription	GM12878-XiMat	blood
25	chr16:48281600-48291000	Weak transcription	Ovary	ovary
26	chr16:48281600-48292800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr16:48281600-48293400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr16:48281800-48288800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr16:48281800-48289000	Weak transcription	Aorta	Aorta
30	chr16:48281800-48289000	Weak transcription	Gastric	stomach
31	chr16:48281800-48289200	Weak transcription	Esophagus	oesophagus
32	chr16:48281800-48313200	Weak transcription	Psoas Muscle	Psoas
33	chr16:48282000-48290400	Weak transcription	HMEC	breast
34	chr16:48282200-48297200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr16:48284200-48291600	Weak transcription	Lung	lung
36	chr16:48284200-48291600	Weak transcription	Pancreas	Pancrea
37	chr16:48285200-48294400	Weak transcription	Colon Smooth Muscle	Colon
38	chr16:48285200-48309600	Strong transcription	HepG2	liver
39	chr16:48285400-48290800	Strong transcription	Primary T cells from cord blood	blood
40	chr16:48285400-48293400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr16:48285600-48288800	Weak transcription	Brain Angular Gyrus	brain
42	chr16:48285600-48290000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr16:48285600-48292600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr16:48285800-48288800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr16:48285800-48290000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr16:48285800-48290000	Strong transcription	Fetal Muscle Trunk	muscle
47	chr16:48285800-48297000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr16:48285800-48298600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr16:48285800-48306800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr16:48285800-48309600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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