Variant report

Variant	rs589611
Chromosome Location	chr15:54819565-54819566
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10152437	0.85[CEU][hapmap]
rs10468008	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10518767	0.84[CEU][hapmap]
rs11071072	0.92[CEU][hapmap]
rs11071087	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11639005	0.88[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs11639014	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12437724	0.95[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap]
rs12443186	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12900512	0.81[ASN][1000 genomes]
rs12908706	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs12909682	0.95[CHB][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap]
rs12910464	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12914472	0.95[CHB][hapmap];0.80[JPT][hapmap]
rs12915430	0.84[CEU][hapmap]
rs12916571	0.84[CEU][hapmap]
rs12916626	0.91[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1356858	0.88[CEU][hapmap]
rs16974753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1818705	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1851007	0.82[ASN][1000 genomes]
rs1851008	0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs1973747	0.81[ASN][1000 genomes]
rs2056342	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2456976	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2899546	1.00[CEU][hapmap]
rs4109295	1.00[CEU][hapmap]
rs4776234	0.84[CEU][hapmap]
rs495769	1.00[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs533450	0.96[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs537389	0.81[CEU][hapmap]
rs540090	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs543451	0.84[EUR][1000 genomes]
rs546169	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs605869	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs640442	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6493687	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs6493690	0.82[ASN][1000 genomes]
rs7163424	0.81[CHB][hapmap];0.84[MEX][hapmap]
rs8023595	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs8023918	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs8026697	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8028630	0.89[MEX][hapmap]
rs8032415	0.88[CEU][hapmap]
rs8039515	0.88[CEU][hapmap]
rs8041282	1.00[CHB][hapmap]
rs8042341	0.95[CHB][hapmap]
rs9302181	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817539	chr15:54132584-55095235	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1038660	chr15:54756184-55039913	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs589611	KIAA1370	cis	parietal	SCAN
rs589611	DYX1C1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54807000-54820600	Weak transcription	Fetal Brain Male	brain
2	chr15:54811000-54869600	Weak transcription	Aorta	Aorta
3	chr15:54818400-54825600	Weak transcription	Fetal Lung	lung
4	chr15:54819200-54819600	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr15:54819200-54819600	Enhancers	H9 Cell Line	embryonic stem cell
6	chr15:54819200-54819600	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr15:54819200-54819600	Enhancers	HUES64 Cell Line	embryonic stem cell

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