Variant report

Variant	rs6445754
Chromosome Location	chr3:55807255-55807256
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2315942	0.84[EUR][1000 genomes]
rs4459870	0.89[EUR][1000 genomes]
rs4542991	0.81[EUR][1000 genomes]
rs4572738	0.81[EUR][1000 genomes]
rs4955882	0.89[EUR][1000 genomes]
rs4955884	0.88[EUR][1000 genomes]
rs4974113	0.88[EUR][1000 genomes]
rs7615473	0.88[EUR][1000 genomes]
rs9809248	0.81[EUR][1000 genomes]
rs9840522	0.88[EUR][1000 genomes]
rs9860951	0.88[EUR][1000 genomes]
rs9879933	0.84[EUR][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	nsv876814	chr3:55802749-55860526	Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Acute lymphoblastic leukemia (childhood)	22076464	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6445754	HESX1	cis	cerebellum	SCAN
rs6445754	CCDC66	cis	parietal	SCAN
rs6445754	TWF2	cis	parietal	SCAN
rs6445754	RRP9	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:55805800-55808000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:55807200-55807400	Enhancers	iPS DF 6.9 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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