Variant report

Variant	rs30088
Chromosome Location	chr5:52425841-52425842
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs152944	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1823072	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs251331	0.91[CEU][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs251335	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs251336	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs251337	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs251338	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs254614	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs254617	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs254618	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs30093	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv880957	chr5:52418582-52443231	Enhancers Weak transcription Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs30088	GZMK	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52421000-52426200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:52423000-52426200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr5:52423000-52426200	Weak transcription	NH-A	brain
4	chr5:52423000-52426200	Weak transcription	NHEK	skin
5	chr5:52423200-52426200	Weak transcription	Osteobl	bone
6	chr5:52425400-52426600	Enhancers	NHLF	lung
7	chr5:52425400-52428000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:52425400-52428400	Enhancers	NHDF-Ad	bronchial
9	chr5:52425600-52428200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:52425800-52426400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:52425800-52426800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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Input of quick search could be:

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

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