Variant report

Variant	rs1416346
Chromosome Location	chr1:58575317-58575318
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10493244	1.00[CEU][hapmap];0.86[CHB][hapmap]
rs1106366	0.91[CEU][hapmap];0.81[TSI][hapmap]
rs1106367	0.91[CEU][hapmap]
rs11207168	0.91[CEU][hapmap];0.81[TSI][hapmap]
rs11207169	0.91[CEU][hapmap];0.81[TSI][hapmap]
rs11207170	0.91[CEU][hapmap]
rs11799299	1.00[CEU][hapmap]
rs11802821	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs12040062	0.84[CEU][hapmap]
rs12042276	0.84[CEU][hapmap]
rs12048970	1.00[CEU][hapmap]
rs12058945	0.91[CEU][hapmap]
rs1213764	0.91[CEU][hapmap]
rs1213770	0.91[CEU][hapmap];0.87[TSI][hapmap]
rs1213771	0.91[CEU][hapmap]
rs1320555	0.91[CEU][hapmap];0.90[MEX][hapmap];0.81[EUR][1000 genomes]
rs13374932	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1342875	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1359494	0.81[CEU][hapmap]
rs1359495	0.91[CEU][hapmap]
rs1416341	0.84[CEU][hapmap]
rs1416343	0.91[CEU][hapmap]
rs17116847	0.91[CEU][hapmap];0.81[TSI][hapmap]
rs17116867	0.91[CEU][hapmap]
rs17116869	0.91[CEU][hapmap]
rs17116983	1.00[CEU][hapmap];0.86[CHB][hapmap]
rs17116988	1.00[CEU][hapmap];0.86[CHB][hapmap]
rs17117013	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs17117039	1.00[CEU][hapmap]
rs17117101	1.00[CEU][hapmap]
rs17117119	0.91[CEU][hapmap]
rs1776184	0.91[CEU][hapmap];0.81[TSI][hapmap]
rs1776192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1832488	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1832489	1.00[CEU][hapmap]
rs1953811	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1992481	0.91[CEU][hapmap]
rs2406591	0.84[CEU][hapmap]
rs2797608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850534	0.84[CEU][hapmap]
rs3850535	1.00[CEU][hapmap];0.86[CHB][hapmap]
rs3861823	0.91[CEU][hapmap]
rs3905539	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs4320799	0.91[CEU][hapmap]
rs7522031	0.91[CEU][hapmap]
rs7551611	1.00[CEU][hapmap]
rs821526	0.83[EUR][1000 genomes]
rs821527	0.91[CEU][hapmap];0.81[TSI][hapmap]
rs821528	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs821529	0.91[CEU][hapmap];0.84[TSI][hapmap]
rs821530	0.86[CEU][hapmap];0.84[TSI][hapmap]
rs873989	0.91[CEU][hapmap];0.81[TSI][hapmap]
rs946310	0.91[CEU][hapmap];0.90[MEX][hapmap];0.81[EUR][1000 genomes]
rs9782935	0.91[CEU][hapmap]

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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1416346	PCSK9	cis	parietal	SCAN
rs1416346	DAB1	cis	cerebellum	SCAN
rs1416346	USP24	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58570000-58576000	Enhancers	GM12878-XiMat	blood
2	chr1:58574000-58576600	Weak transcription	Thymus	Thymus
3	chr1:58575000-58575600	Enhancers	Fetal Thymus	thymus

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