Variant report

Variant	rs552017
Chromosome Location	chr11:84993643-84993644
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:84988076..84990491-chr11:84991343..84993778,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10501590	0.85[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap]
rs10792810	0.84[ASW][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs1400630	0.85[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap]
rs1517308	0.84[ASW][hapmap];0.86[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1517310	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1517317	0.82[JPT][hapmap]
rs1914375	0.87[JPT][hapmap]
rs2000962	0.90[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap]
rs2203702	0.84[ASW][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs2449987	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs286045	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs286048	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs286052	0.81[ASN][1000 genomes]
rs286515	0.96[MEX][hapmap]
rs349077	0.83[JPT][hapmap]
rs454388	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs471786	0.83[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs472630	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4944512	0.90[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs530323	0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.85[LWK][hapmap];0.88[ASN][1000 genomes]
rs534604	0.80[AMR][1000 genomes]
rs552373	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs556710	0.85[ASN][1000 genomes]
rs563788	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580188	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs601857	0.84[ASW][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap]
rs789600	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7935720	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs938727	0.84[ASW][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9734338	0.87[JPT][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	nsv1044370	chr11:84748993-85293233	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv898043	chr11:84895033-85148689	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv898044	chr11:84895033-85220773	ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs552017	LHX2	trans	lymphoblastoid	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:84967800-85019400	Weak transcription	Ovary	ovary
2	chr11:84974800-84998400	Weak transcription	HSMMtube	muscle

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