Variant report

Variant	rs39889
Chromosome Location	chr5:16717078-16717079
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:16710425..16712025-chr5:16715112..16717325,2	MCF-7	breast:
2	chr5:16713673..16715499-chr5:16715772..16717770,2	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs152726	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs153182	0.81[AMR][1000 genomes]
rs153183	0.81[AMR][1000 genomes]
rs153184	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs153185	0.88[ASN][1000 genomes]
rs193924	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs250343	0.81[ASN][1000 genomes]
rs27552	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs31290	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs31296	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs31297	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs31299	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs31497	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs42564	0.88[ASN][1000 genomes]
rs506740	0.80[AMR][1000 genomes];0.82[EUR][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	nsv869660	chr5:16651289-16766428	Genic enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv880373	chr5:16710572-16785604	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16682400-16736000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:16710400-16723600	Weak transcription	Esophagus	oesophagus
3	chr5:16711200-16719000	Weak transcription	Lung	lung
4	chr5:16711200-16719400	Weak transcription	Pancreas	Pancrea
5	chr5:16711200-16723800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:16711200-16736400	Weak transcription	Hela-S3	cervix
7	chr5:16711400-16717600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr5:16711400-16719400	Weak transcription	Gastric	stomach
9	chr5:16711400-16721000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:16711400-16721200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr5:16711400-16721600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:16711400-16724000	Weak transcription	Ovary	ovary
13	chr5:16711400-16727800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr5:16711400-16728200	Weak transcription	Spleen	Spleen
15	chr5:16711400-16730200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:16711400-16731800	Weak transcription	HMEC	breast
17	chr5:16711600-16721600	Weak transcription	NHEK	skin
18	chr5:16711600-16721800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:16711600-16736000	Weak transcription	Placenta	Placenta
20	chr5:16713600-16721600	Weak transcription	Stomach Mucosa	stomach
21	chr5:16713800-16719200	Weak transcription	HepG2	liver
22	chr5:16713800-16731600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:16713800-16735600	Weak transcription	Colonic Mucosa	Colon
24	chr5:16714000-16717400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr5:16714000-16717400	Weak transcription	Fetal Intestine Large	intestine
26	chr5:16714000-16719800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr5:16714000-16721400	Weak transcription	HSMMtube	muscle
28	chr5:16714000-16721600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:16714000-16724000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr5:16714000-16726200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr5:16714000-16726200	Weak transcription	Left Ventricle	heart
32	chr5:16714000-16730200	Weak transcription	Osteobl	bone
33	chr5:16714200-16717400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr5:16714200-16718000	Weak transcription	Fetal Stomach	stomach
35	chr5:16714200-16718400	Weak transcription	Fetal Intestine Small	intestine
36	chr5:16714200-16721400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:16714200-16721600	Weak transcription	Fetal Lung	lung
38	chr5:16714200-16721600	Weak transcription	A549	lung
39	chr5:16714200-16721600	Weak transcription	HSMM	muscle
40	chr5:16714200-16726200	Weak transcription	Fetal Kidney	kidney
41	chr5:16714200-16730400	Weak transcription	NHLF	lung
42	chr5:16714200-16736000	Weak transcription	NHDF-Ad	bronchial
43	chr5:16714400-16720200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr5:16714400-16721200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr5:16714400-16730000	Weak transcription	NH-A	brain
46	chr5:16714600-16717400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr5:16714600-16717800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr5:16714600-16719400	Weak transcription	Brain Anterior Caudate	brain
49	chr5:16714600-16720200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:16714600-16721600	Weak transcription	Brain Angular Gyrus	brain

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