Variant report

Variant	rs454388
Chromosome Location	chr11:85087410-85087411
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10501590	0.85[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.82[YRI][hapmap]
rs10751124	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10792810	0.84[ASW][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap]
rs1400630	0.85[CHB][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap]
rs1517308	0.84[ASW][hapmap];0.86[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap]
rs1517310	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs1517317	0.86[JPT][hapmap]
rs1605898	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1914375	0.91[JPT][hapmap]
rs2000962	0.90[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap]
rs2203702	0.84[ASW][hapmap];0.90[CHB][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap]
rs2449987	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs286045	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286047	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs286048	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286050	0.82[ASN][1000 genomes]
rs286051	0.82[ASN][1000 genomes]
rs286052	0.82[ASN][1000 genomes]
rs286515	0.83[MEX][hapmap];0.86[AMR][1000 genomes]
rs371815	0.81[ASN][1000 genomes]
rs393308	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs405726	0.90[ASN][1000 genomes]
rs450444	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs471786	0.83[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.84[ASN][1000 genomes]
rs472630	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4944512	0.90[CHB][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap]
rs530323	0.81[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs552017	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs552373	0.81[ASN][1000 genomes]
rs563788	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs580188	0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs601857	0.84[ASW][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap]
rs720496	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs789600	0.81[ASN][1000 genomes]
rs7935720	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs938727	0.84[ASW][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap]
rs9734338	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv1051155	chr11:85006564-85721261	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv541110	chr11:85006564-85721261	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs454388	LHX2	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85085000-85089200	Weak transcription	Fetal Muscle Trunk	muscle

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