Variant report

Variant	rs2279980
Chromosome Location	chr5:57913379-57913380
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10060568	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1158196	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs12054892	1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs12653046	1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs13354637	1.00[CEU][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16877131	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1833611	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs58662773	0.89[EUR][1000 genomes]
rs59064450	0.90[EUR][1000 genomes]
rs6898044	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs72760264	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7723730	0.86[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	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1029145	chr5:57905821-58141221	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830311	chr5:57912546-58105636	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2279980	MAP3K1	cis	parietal	SCAN
rs2279980	GAPT	cis	parietal	SCAN
rs2279980	CDC20B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57912600-57913400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:57912600-57913400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:57913000-57913600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr5:57913200-57913600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr5:57913200-57914000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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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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