Variant report

Variant	rs12548661
Chromosome Location	chr8:130452076-130452077
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10099692	0.80[MEX][hapmap]
rs10956477	0.87[GIH][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12543679	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13259353	0.97[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13262640	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13269801	0.92[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1368139	0.87[GIH][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs16904062	0.85[ASW][hapmap];0.92[GIH][hapmap];0.92[TSI][hapmap]
rs16904064	0.85[ASW][hapmap];0.92[GIH][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs1813473	0.97[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1897447	0.80[MEX][hapmap]
rs28759297	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35938360	0.83[EUR][1000 genomes]
rs970451	0.84[MEX][hapmap]
rs985687	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429942	chr8:130397818-130460011	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1015611	chr8:130449321-130502086	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12548661	OC90	cis	cerebellum	SCAN
rs12548661	PHF20L1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:130448600-130458800	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr8:130449400-130452800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr8:130451000-130452200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr8:130451400-130462000	Weak transcription	Thymus	Thymus
5	chr8:130451600-130452600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr8:130451800-130452800	Enhancers	Adipose Nuclei	Adipose
7	chr8:130452000-130454200	Genic enhancers	K562	blood

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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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