Variant report

Variant	rs16880627
Chromosome Location	chr5:52295877-52295878
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	chr5:52285803..52288356-chr5:52293284..52295985,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249899	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10461562	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12518145	1.00[YRI][hapmap]
rs12520591	1.00[YRI][hapmap]
rs1363190	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1363191	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs1445937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16880493	1.00[YRI][hapmap]
rs2279584	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2279586	1.00[YRI][hapmap]
rs2279587	1.00[YRI][hapmap]
rs2302960	1.00[YRI][hapmap]
rs2897456	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3212392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212404	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3212424	0.83[JPT][hapmap]
rs3212657	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs41315912	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4145748	1.00[YRI][hapmap]
rs6867926	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7701575	1.00[YRI][hapmap]
rs7703474	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7705061	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7717360	0.91[EUR][1000 genomes]
rs9637769	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv880425	chr5:52291279-52345868	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52286200-52300400	Weak transcription	Gastric	stomach
2	chr5:52286200-52303400	Weak transcription	Small Intestine	intestine
3	chr5:52286200-52313600	Weak transcription	Lung	lung
4	chr5:52286600-52300000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr5:52286600-52302400	Weak transcription	Fetal Stomach	stomach
6	chr5:52286800-52298800	Weak transcription	Fetal Intestine Large	intestine
7	chr5:52287000-52299400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr5:52289200-52311600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:52290000-52299800	Weak transcription	NH-A	brain
10	chr5:52292400-52299200	Weak transcription	Esophagus	oesophagus
11	chr5:52292400-52301000	Weak transcription	Spleen	Spleen
12	chr5:52292400-52303200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr5:52293600-52297400	Weak transcription	HUVEC	blood vessel
14	chr5:52293600-52304000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr5:52293800-52296000	Enhancers	A549	lung
16	chr5:52293800-52298800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr5:52293800-52299200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr5:52293800-52313400	Weak transcription	Fetal Intestine Small	intestine
19	chr5:52294000-52296400	Enhancers	Brain Substantia Nigra	brain
20	chr5:52294200-52296400	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr5:52294200-52297400	Enhancers	Brain Hippocampus Middle	brain
22	chr5:52294200-52301200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:52294400-52296000	Enhancers	NHDF-Ad	bronchial
24	chr5:52294400-52297200	Genic enhancers	HepG2	liver
25	chr5:52294600-52302400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr5:52294600-52302600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr5:52294600-52302800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr5:52295000-52296000	Enhancers	Osteobl	bone
29	chr5:52295400-52296000	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr5:52295600-52296000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:52295600-52296200	Strong transcription	HMEC	breast
32	chr5:52295600-52296400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr5:52295600-52296400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr5:52295600-52297000	Weak transcription	NHEK	skin
35	chr5:52295600-52297000	Weak transcription	NHLF	lung
36	chr5:52295600-52297200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr5:52295600-52297200	Weak transcription	Hela-S3	cervix
38	chr5:52295600-52299000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:52295600-52299800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr5:52295800-52296200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr5:52295800-52296600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:52295800-52297000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr5:52295800-52297000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr5:52295800-52297200	Weak transcription	Brain Angular Gyrus	brain
45	chr5:52295800-52298800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr5:52295800-52300200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:52295800-52303000	Weak transcription	Brain Anterior Caudate	brain

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