Variant report

Variant	rs2817739
Chromosome Location	chr6:24760958-24760959
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12214068	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1555430	0.87[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2064976	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2145752	0.96[CEU][hapmap];0.80[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2754770	0.82[AFR][1000 genomes]
rs2754776	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2754777	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2817728	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2817732	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][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	nsv830609	chr6:24712086-24896647	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv428474	chr6:24714157-24797977	Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv965630	chr6:24745410-24767271	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2817739	CMAH	cis	lymphoblastoid	seeQTL
rs2817739	HIST1H4G	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24754000-24761400	Weak transcription	Stomach Mucosa	stomach
2	chr6:24756000-24761800	Weak transcription	Hela-S3	cervix
3	chr6:24757000-24761200	Weak transcription	K562	blood
4	chr6:24760400-24775000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:24760800-24762200	Enhancers	HepG2	liver

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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