Variant report

Variant	rs12040062
Chromosome Location	chr1:58586505-58586506
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10493244	0.84[CEU][hapmap]
rs11799299	0.84[CEU][hapmap]
rs11802821	0.84[CEU][hapmap];0.83[TSI][hapmap]
rs12025945	0.94[ASN][1000 genomes]
rs12034198	0.92[ASN][1000 genomes]
rs12042276	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12048970	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12565597	0.90[ASN][1000 genomes]
rs13374932	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs1342875	0.84[CEU][hapmap]
rs1416341	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1416343	0.91[JPT][hapmap]
rs1416346	0.84[CEU][hapmap]
rs1418765	0.94[ASN][1000 genomes]
rs17116983	0.84[CEU][hapmap];0.80[CHD][hapmap];0.84[TSI][hapmap]
rs17116988	0.84[CEU][hapmap];0.80[CHD][hapmap];0.84[TSI][hapmap]
rs17117013	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs17117039	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs17117101	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs1776192	0.83[CEU][hapmap]
rs1832489	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs1953811	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs2225949	0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs2406591	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2797608	0.82[CEU][hapmap]
rs3850534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3850535	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs3905539	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs6667829	0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6701275	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74074998	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74076076	0.80[EUR][1000 genomes]
rs7551611	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv530017	chr1:58002290-58669736	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv431379	chr1:58224212-58802608	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1008968	chr1:58582159-58982440	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv534974	chr1:58582159-58982440	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv525581	chr1:58582979-58598226	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12040062	DAB1	cis	cerebellum	SCAN
rs12040062	PCSK9	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58586000-58587200	Weak transcription	Thymus	Thymus

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