Variant report

Variant	rs12048970
Chromosome Location	chr1:58590073-58590074
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10493244	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1106366	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs1106367	0.91[CEU][hapmap]
rs11207168	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs11207169	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs11207170	0.91[CEU][hapmap]
rs11799299	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11799320	0.88[EUR][1000 genomes]
rs11801568	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11802821	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11809707	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12025945	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12034198	0.90[ASN][1000 genomes]
rs12040062	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]
rs12042276	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12058945	0.91[CEU][hapmap]
rs1213764	0.91[CEU][hapmap]
rs1213770	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs1213771	0.91[CEU][hapmap]
rs12565486	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12565597	0.88[ASN][1000 genomes]
rs1320555	0.91[CEU][hapmap]
rs13374932	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs1342875	1.00[CEU][hapmap]
rs1359494	0.81[CEU][hapmap]
rs1359495	0.91[CEU][hapmap]
rs1416341	0.84[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs1416343	0.91[CEU][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs1416344	0.81[EUR][1000 genomes]
rs1416346	1.00[CEU][hapmap]
rs1418765	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17116847	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs17116867	0.91[CEU][hapmap]
rs17116869	0.91[CEU][hapmap]
rs17116983	1.00[CEU][hapmap];0.80[CHD][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap]
rs17116988	1.00[CEU][hapmap];0.80[CHD][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17117013	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17117039	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17117101	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs17117108	0.88[EUR][1000 genomes]
rs17117119	0.91[CEU][hapmap]
rs17117128	0.81[EUR][1000 genomes]
rs1776184	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs1776192	1.00[CEU][hapmap]
rs1832488	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1832489	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs1953811	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs1992481	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs2225949	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs2406591	0.84[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs2797608	1.00[CEU][hapmap]
rs35995264	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3850534	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3850535	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3850536	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3861823	0.91[CEU][hapmap]
rs3905539	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs4320799	0.91[CEU][hapmap]
rs4406656	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59675977	0.88[EUR][1000 genomes]
rs59994009	0.88[EUR][1000 genomes]
rs60060991	0.88[EUR][1000 genomes]
rs60112110	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6667829	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6701275	0.90[ASN][1000 genomes]
rs74074110	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs74074991	0.90[EUR][1000 genomes]
rs74074993	0.88[EUR][1000 genomes]
rs74075932	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs74075933	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs74075935	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs74075938	0.89[EUR][1000 genomes]
rs74076072	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs74076075	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs74076076	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs74076078	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7522031	0.91[CEU][hapmap]
rs7551611	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs821527	0.91[CEU][hapmap]
rs821528	0.91[CEU][hapmap]
rs821529	0.91[CEU][hapmap];0.81[TSI][hapmap]
rs821530	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs873989	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs946310	0.91[CEU][hapmap]
rs9782935	0.91[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
rs12048970	PCSK9	cis	parietal	SCAN
rs12048970	USP24	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58589400-58590600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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