Variant report

Variant	rs3860324
Chromosome Location	chr1:221809552-221809553
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1018334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10442685	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10863640	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11118777	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11118778	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12023780	0.92[CEU][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12026281	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12029530	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12029601	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12136513	0.90[AFR][1000 genomes]
rs12748524	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12753128	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1879068	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1933268	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2176690	0.81[AFR][1000 genomes]
rs2378461	0.90[AFR][1000 genomes]
rs4436399	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4450027	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4484930	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6658414	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6658755	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6663135	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6663415	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6663637	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6666514	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6677071	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6697462	0.92[CEU][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7540426	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv873200	chr1:221644180-221843191	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1011037	chr1:221756526-221809552	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3860324	LYPLAL1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221806000-221811200	Weak transcription	Fetal Heart	heart
2	chr1:221806200-221813600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:221809200-221811000	Weak transcription	HMEC	breast

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