Variant report

Variant	rs62257495
Chromosome Location	chr3:78868229-78868230
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11127635	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11712472	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11713976	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11718731	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12633168	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12633926	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12638686	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13065160	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13071446	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13083478	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs162818	0.89[ASN][1000 genomes]
rs162869	0.81[ASN][1000 genomes]
rs17016554	0.82[AFR][1000 genomes]
rs1970807	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs333472	0.85[ASN][1000 genomes]
rs333490	0.81[ASN][1000 genomes]
rs34494591	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35056070	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35763568	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35891410	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35984348	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3856695	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs424737	0.85[ASN][1000 genomes]
rs444992	0.85[ASN][1000 genomes]
rs60860653	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62257492	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62257496	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6773457	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7611402	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7627461	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9637502	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][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	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv877019	chr3:78808850-78877217	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv432459	chr3:78819310-78874310	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78851400-78880400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:78854200-78872600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:78854400-78871200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:78855400-78872600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:78860200-78871600	Weak transcription	HepG2	liver
6	chr3:78860800-78869600	Weak transcription	Fetal Brain Male	brain
7	chr3:78861000-78872600	Weak transcription	Brain Anterior Caudate	brain
8	chr3:78861800-78869800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:78862400-78869600	Weak transcription	Fetal Lung	lung
10	chr3:78864800-78868800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:78865400-78869600	Weak transcription	Fetal Heart	heart
12	chr3:78866000-78868800	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:78866000-78872800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:78867600-78875200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:78867800-78871800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:78867800-78872600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:78868000-78871000	Weak transcription	Fetal Muscle Leg	muscle
18	chr3:78868000-78871400	Weak transcription	Fetal Stomach	stomach
19	chr3:78868000-78881600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:78868200-78870000	Enhancers	Brain Substantia Nigra	brain
21	chr3:78868200-78870200	Enhancers	Brain Cingulate Gyrus	brain

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