Variant report

Variant	rs333509
Chromosome Location	chr3:78843524-78843525
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12330466	1.00[AMR][1000 genomes]
rs12330828	1.00[AMR][1000 genomes]
rs13319888	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs162816	1.00[AMR][1000 genomes]
rs173004	1.00[AMR][1000 genomes]
rs231606	1.00[AMR][1000 genomes]
rs333473	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs333482	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs333492	1.00[AMR][1000 genomes]
rs333494	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs333496	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs333500	1.00[AMR][1000 genomes]
rs333504	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs333505	1.00[AMR][1000 genomes]
rs333510	0.83[AFR][1000 genomes]
rs365492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs365924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs375298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs383189	1.00[AMR][1000 genomes]
rs390060	1.00[AMR][1000 genomes]
rs408455	1.00[AMR][1000 genomes]
rs416640	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72892483	1.00[AMR][1000 genomes]
rs72896415	1.00[AMR][1000 genomes]
rs9631524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9631525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9810277	1.00[AMR][1000 genomes]
rs9813851	1.00[AMR][1000 genomes]
rs9817612	1.00[AMR][1000 genomes]
rs9822237	1.00[AMR][1000 genomes]
rs9849099	1.00[AMR][1000 genomes]
rs9872311	1.00[AMR][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:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78826600-78843600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:78835000-78843600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:78835200-78843800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:78838800-78843600	Weak transcription	NHEK	skin
5	chr3:78840400-78843600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:78841200-78845800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:78841200-78850600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:78841400-78851600	Weak transcription	Brain Anterior Caudate	brain
9	chr3:78841600-78850800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:78842800-78843600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:78842800-78845600	Weak transcription	Brain Angular Gyrus	brain
12	chr3:78842800-78846200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:78843000-78845800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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