Variant report

Variant	rs6543739
Chromosome Location	chr2:33936701-33936702
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1448556	0.81[EUR][1000 genomes]
rs1550992	0.92[CEU][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes]
rs1868348	0.83[EUR][1000 genomes]
rs1900775	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6543738	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6715757	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7574123	0.83[MEX][hapmap]
rs7585657	0.92[CEU][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs7588769	0.86[EUR][1000 genomes]

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	esv3350238	chr2:33849408-33979026	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv873793	chr2:33936701-33988173	Weak transcription Enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
3	nsv873794	chr2:33936701-34103546	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6543739	FAM98A	cis	cerebellum	SCAN
rs6543739	HSH2D	trans	parietal	SCAN
rs6543739	TTC27	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33930000-33937400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:33930200-33937000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:33930200-33937000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:33930400-33937000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:33935000-33937600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:33936400-33938000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:33936600-33938400	Enhancers	HUES64 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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