Variant report

Variant	rs3212402
Chromosome Location	chr5:52306044-52306045
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10042752	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10058636	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10061730	0.85[AMR][1000 genomes]
rs10071255	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10071580	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11948978	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421941	0.97[ASN][1000 genomes]
rs16880636	1.00[ASN][1000 genomes]
rs1862639	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212412	1.00[ASN][1000 genomes]
rs3212417	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55783963	1.00[ASN][1000 genomes]
rs67217308	1.00[ASN][1000 genomes]
rs67835512	1.00[ASN][1000 genomes]
rs6883028	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9292002	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9292003	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][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	chr5:52289200-52311600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:52293800-52313400	Weak transcription	Fetal Intestine Small	intestine
4	chr5:52299400-52313400	Weak transcription	Esophagus	oesophagus
5	chr5:52301200-52306800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr5:52302600-52308000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr5:52303000-52307400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:52303200-52306800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr5:52303400-52320400	Weak transcription	Fetal Brain Male	brain
10	chr5:52304000-52306800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:52304800-52307400	Enhancers	HMEC	breast
12	chr5:52304800-52307800	Enhancers	HepG2	liver
13	chr5:52305000-52306800	Weak transcription	NHLF	lung
14	chr5:52305000-52313400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:52305000-52314600	Weak transcription	HUVEC	blood vessel
16	chr5:52305200-52311600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:52305200-52317200	Weak transcription	A549	lung
18	chr5:52305400-52306200	Weak transcription	Hela-S3	cervix
19	chr5:52305400-52307200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:52305400-52313000	Weak transcription	NH-A	brain
21	chr5:52305600-52306800	Enhancers	NHEK	skin
22	chr5:52305800-52306600	Weak transcription	NHDF-Ad	bronchial
23	chr5:52305800-52307400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:52305800-52307400	Enhancers	Brain Hippocampus Middle	brain
25	chr5:52305800-52307800	Enhancers	Brain Cingulate Gyrus	brain
26	chr5:52305800-52311600	Weak transcription	Brain Substantia Nigra	brain
27	chr5:52306000-52306600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:52306000-52307200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr5:52306000-52310000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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