Variant report

Variant	rs1421888
Chromosome Location	chr5:128237416-128237417
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11953704	0.81[AMR][1000 genomes]
rs185411	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes]
rs2526254	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes]
rs257896	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs257897	0.86[CEU][hapmap];0.84[CHB][hapmap]
rs257898	0.90[CEU][hapmap]
rs257899	0.89[CEU][hapmap];0.86[CHB][hapmap]
rs257900	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs257901	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs257903	0.81[AMR][1000 genomes]
rs257908	0.95[CEU][hapmap];1.00[CHB][hapmap];0.80[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes]
rs257999	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes]
rs258000	0.95[CEU][hapmap];1.00[CHB][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs258002	0.81[AMR][1000 genomes]
rs258004	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs976944	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599699	chr5:128172808-128259451	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv462443	chr5:128172808-128298437	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv599700	chr5:128172808-128298437	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv882837	chr5:128200502-128287228	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv882838	chr5:128203439-128287228	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv882839	chr5:128205828-128390167	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv882840	chr5:128205828-128428962	Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	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
rs1421888	ERN1	trans	parietal	SCAN
rs1421888	C5orf48	cis	cerebellum	SCAN
rs1421888	SLC27A6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:128237000-128238200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr5:128237000-128238600	Enhancers	Fetal Heart	heart

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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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