Variant report

Variant	rs1998617
Chromosome Location	chr6:87808614-87808615
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1055409	0.95[CEU][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6909630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6910649	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7738290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7745823	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs7748510	0.95[CEU][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs9294363	0.88[EUR][1000 genomes]
rs9344675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs981087	0.81[MKK][hapmap]

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	nsv1024751	chr6:87433199-87908721	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1998617	C6orf165	cis	cerebellum	SCAN
rs1998617	C6orf162	cis	cerebellum	SCAN
rs1998617	C6orf165	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87803600-87816000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:87805800-87808800	Weak transcription	Hela-S3	cervix
3	chr6:87806000-87810600	Weak transcription	Placenta	Placenta
4	chr6:87807000-87812600	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr6:87808200-87808800	Enhancers	GM12878-XiMat	blood
6	chr6:87808600-87808800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:87808600-87809000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:87808600-87809200	Enhancers	Primary B cells from peripheral blood	blood
9	chr6:87808600-87810000	Enhancers	HepG2	liver

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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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