Variant report

Variant	rs12207402
Chromosome Location	chr6:45246577-45246578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1555681	1.00[YRI][hapmap]
rs17209755	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs3749863	1.00[YRI][hapmap]
rs9395069	1.00[YRI][hapmap]
rs9395084	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs9472487	1.00[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1024370	chr6:44878053-45251451	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1028068	chr6:45169010-45246577	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv2763550	chr6:45186825-45275593	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv830652	chr6:45187467-45328983	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12207402	CYP39A1	cis	parietal	SCAN
rs12207402	CD2AP	cis	parietal	SCAN
rs12207402	RCAN2	cis	cerebellum	SCAN
rs12207402	SUPT3H	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45225600-45248800	Weak transcription	Ovary	ovary
2	chr6:45239200-45248800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:45239200-45248800	Weak transcription	Aorta	Aorta
4	chr6:45239400-45248800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:45239600-45246600	Weak transcription	Primary T cells from cord blood	blood
6	chr6:45239800-45248800	Weak transcription	Fetal Intestine Small	intestine
7	chr6:45240000-45247800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr6:45246400-45246800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	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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