Variant report

Variant	rs12074764
Chromosome Location	chr1:220045654-220045655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs17006764	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17006774	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67024624	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72740952	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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	nsv1006393	chr1:219925261-220126458	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1067840	chr1:219990803-220091941	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12074764	GALNT9	trans	lymphoblastoid	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220044400-220045800	Enhancers	HepG2	liver
2	chr1:220044400-220045800	Enhancers	K562	blood
3	chr1:220044400-220047200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:220044600-220046000	Enhancers	Liver	Liver
5	chr1:220044800-220046200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:220045000-220057200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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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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