Variant report

Variant	rs12300006
Chromosome Location	chr12:44857999-44858000
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10467198	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11182492	0.81[AFR][1000 genomes]
rs11182494	0.81[AFR][1000 genomes]
rs11182503	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12301186	1.00[AMR][1000 genomes]
rs12304363	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12308192	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12310486	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12311300	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12322750	1.00[AMR][1000 genomes]
rs1493757	1.00[AMR][1000 genomes]
rs56009337	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57316311	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59907388	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60037016	1.00[AMR][1000 genomes]
rs60810059	1.00[AMR][1000 genomes]
rs61334019	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74085006	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74085037	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74085043	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74085152	1.00[AMR][1000 genomes]
rs74087530	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9971775	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049818	chr12:44486312-45133783	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12300006	PKP4	trans	lymphoblastoid	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44852200-44859600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:44857000-44858800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:44857200-44858600	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr12:44857200-44858800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:44857400-44858000	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr12:44857400-44858800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr12:44857400-44858800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:44857800-44858200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:44857800-44858400	Enhancers	H1 Cell Line	embryonic stem cell
10	chr12:44857800-44858800	Enhancers	iPS-20b 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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