Variant report

Variant	rs1233487
Chromosome Location	chr6:29468809-29468810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1345228	0.93[ASN][1000 genomes]
rs2021078	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2074466	0.88[ASN][1000 genomes]
rs2074469	0.85[ASN][1000 genomes]
rs2285791	0.97[ASN][1000 genomes]
rs2285792	0.97[ASN][1000 genomes]
rs4713226	0.87[ASN][1000 genomes]
rs4959120	0.90[ASN][1000 genomes]
rs734960	0.99[ASN][1000 genomes]
rs734961	0.99[ASN][1000 genomes]
rs7454176	0.97[ASN][1000 genomes]
rs9257863	0.91[ASN][1000 genomes]
rs9257869	0.96[ASN][1000 genomes]
rs9257873	0.99[ASN][1000 genomes]
rs9257874	0.99[ASN][1000 genomes]
rs9257879	0.95[ASN][1000 genomes]
rs9257886	0.95[ASN][1000 genomes]
rs9257889	0.97[ASN][1000 genomes]
rs9257890	0.97[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	esv3424039	chr6:29439297-29504564	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv883528	chr6:29447724-29494897	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv883529	chr6:29464365-29494897	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1233487	HLA-A	cis	brain	seeQTL
rs1233487	HIST1H2BM	cis	cerebellum	SCAN
rs1233487	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs1233487	ZSCAN23	cis	parietal	SCAN
rs1233487	ZSCAN23	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29468600-29496200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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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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