Variant report

Variant	rs7769128
Chromosome Location	chr6:44334388-44334389
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10948132	0.82[CEU][hapmap];0.92[TSI][hapmap]
rs1122627	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1411903	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411904	0.91[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1909887	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2065361	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711780	0.88[YRI][hapmap]
rs6935721	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7769100	0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9462982	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9462983	0.86[EUR][1000 genomes]
rs9472259	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9472261	0.90[AMR][1000 genomes];0.84[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	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv1019145	chr6:44313576-44421440	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1794353	chr6:44333489-44350716	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7769128	MED20	cis	parietal	SCAN
rs7769128	RRP36	cis	cerebellum	SCAN
rs7769128	PEX6	cis	cerebellum	SCAN
rs7769128	CD2AP	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44334200-44334800	Enhancers	HepG2	liver
2	chr6:44334200-44335400	Enhancers	Liver	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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