Variant report

Variant	rs6667442
Chromosome Location	chr1:213638762-213638763
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11120128	0.90[JPT][hapmap];0.90[YRI][hapmap]
rs11120134	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11120135	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1158048	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12036568	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1434893	1.00[CEU][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap]
rs2083325	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6540789	0.82[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[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	nsv832525	chr1:213580476-213782815	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv524186	chr1:213637483-213641943	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv526119	chr1:213637483-213652148	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6667442	LOC148696	cis	cerebellum	SCAN
rs6667442	PPP2R5A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213638000-213640000	Enhancers	NHEK	skin
2	chr1:213638200-213639000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:213638200-213639400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:213638200-213639400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:213638200-213640000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:213638200-213640200	Enhancers	Placenta Amnion	Placenta Amnion
7	chr1:213638400-213638800	Enhancers	HMEC	breast

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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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