Variant report

Variant	rs6548012
Chromosome Location	chr2:30599808-30599809
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10514770	0.80[EUR][1000 genomes]
rs11127273	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13000021	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13033921	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4519571	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6548013	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6756908	0.83[LWK][hapmap]
rs7572690	0.89[CEU][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7583194	0.93[EUR][1000 genomes]
rs7583844	0.88[EUR][1000 genomes]
rs7593766	0.80[EUR][1000 genomes]
rs829588	0.92[EUR][1000 genomes]
rs829610	0.81[CEU][hapmap];0.89[GIH][hapmap]
rs829611	0.81[CEU][hapmap]
rs829612	0.85[CEU][hapmap];0.91[GIH][hapmap]
rs829613	0.81[CEU][hapmap]
rs829614	0.85[CEU][hapmap]

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	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv833648	chr2:30505882-30696275	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv873769	chr2:30585638-30625264	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6548012	CHCHD3	trans	cerebellum	SCAN
rs6548012	EIF1AY	trans	lymphoblastoid	seeQTL
rs6548012	PREB	cis	parietal	SCAN
rs6548012	RPS4Y1	trans	lymphoblastoid	seeQTL
rs6548012	DDX3Y	trans	lymphoblastoid	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30585600-30605800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:30593000-30601000	Weak transcription	Pancreas	Pancrea

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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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