Variant report

Variant	rs2897456
Chromosome Location	chr5:52312351-52312352
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10461562	0.84[ASN][1000 genomes]
rs12518145	1.00[YRI][hapmap]
rs12520591	1.00[YRI][hapmap]
rs1363190	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1363191	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1445937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16880493	1.00[YRI][hapmap]
rs16880627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2056401	0.82[EUR][1000 genomes]
rs2056402	0.82[EUR][1000 genomes]
rs2279584	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes]
rs2279586	1.00[YRI][hapmap]
rs2279587	1.00[YRI][hapmap]
rs2302960	1.00[YRI][hapmap]
rs3212392	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3212404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212475	0.81[EUR][1000 genomes]
rs3212531	0.81[EUR][1000 genomes]
rs3212657	1.00[CEU][hapmap]
rs3212692	0.82[EUR][1000 genomes]
rs41315912	0.86[EUR][1000 genomes]
rs4145748	1.00[YRI][hapmap]
rs6867926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7701575	1.00[YRI][hapmap]
rs7703474	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7705061	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7717360	0.85[EUR][1000 genomes]
rs9637769	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][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:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52286200-52313600	Weak transcription	Lung	lung
2	chr5:52293800-52313400	Weak transcription	Fetal Intestine Small	intestine
3	chr5:52299400-52313400	Weak transcription	Esophagus	oesophagus
4	chr5:52303400-52320400	Weak transcription	Fetal Brain Male	brain
5	chr5:52305000-52313400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:52305000-52314600	Weak transcription	HUVEC	blood vessel
7	chr5:52305200-52317200	Weak transcription	A549	lung
8	chr5:52305400-52313000	Weak transcription	NH-A	brain
9	chr5:52306800-52313000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:52307000-52333800	Weak transcription	Gastric	stomach
11	chr5:52307400-52312800	Weak transcription	HMEC	breast
12	chr5:52307400-52313000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:52307400-52313000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:52307400-52313000	Weak transcription	NHDF-Ad	bronchial
15	chr5:52307800-52313800	Weak transcription	NHEK	skin
16	chr5:52308800-52313600	Enhancers	HepG2	liver
17	chr5:52310000-52312800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:52310000-52313200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:52310800-52315000	Enhancers	Hela-S3	cervix
20	chr5:52311000-52313200	Enhancers	Brain Cingulate Gyrus	brain
21	chr5:52311000-52314200	Enhancers	Brain Hippocampus Middle	brain
22	chr5:52311400-52313200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:52311400-52314000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr5:52311600-52314200	Enhancers	Brain Substantia Nigra	brain
25	chr5:52311800-52317200	Weak transcription	NHLF	lung
26	chr5:52312000-52314000	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr5:52312000-52318400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr5:52312200-52312400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr5:52312200-52312800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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