Variant report

Variant	rs4704200
Chromosome Location	chr5:74569856-74569857
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10070119	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10942734	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11749783	0.90[GIH][hapmap]
rs11957260	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12654264	0.80[CHD][hapmap];0.88[GIH][hapmap]
rs12916	0.82[CHD][hapmap]
rs1423527	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2112653	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2126736	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2335418	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2878417	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs3846662	0.85[CEU][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap]
rs3846663	0.82[CHD][hapmap]
rs4704202	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6878990	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs6892023	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7702895	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7703051	0.90[GIH][hapmap]
rs7722186	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv1016610	chr5:74403611-74627654	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2758000	chr5:74433760-74611714	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2759350	chr5:74433760-74611714	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4704200	HMGCR	cis	cerebellum	SCAN
rs4704200	HMGCR	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74568400-74579400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:74569200-74570800	Weak transcription	Colonic Mucosa	Colon
3	chr5:74569200-74573200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:74569400-74570200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell

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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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