Variant report

Variant	rs512910
Chromosome Location	chr11:85007026-85007027
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10898380	0.88[ASW][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10898382	0.82[ASW][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap]
rs11234316	0.84[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap]
rs12419394	0.85[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1517311	0.90[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap]
rs1682383	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17810088	0.84[CHB][hapmap]
rs1793210	0.86[ASN][1000 genomes]
rs1826612	0.88[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1914373	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1914376	0.89[ASN][1000 genomes]
rs2138748	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs286044	0.84[ASN][1000 genomes]
rs286499	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs286513	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs286515	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap]
rs2930575	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35167573	0.83[ASN][1000 genomes]
rs473968	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474992	0.89[ASN][1000 genomes]
rs475164	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476781	0.94[ASN][1000 genomes]
rs488668	0.90[ASN][1000 genomes]
rs4943918	0.89[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap]
rs4944513	0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs495905	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs496814	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs497607	0.94[ASN][1000 genomes]
rs500307	0.90[ASN][1000 genomes]
rs508177	0.91[ASN][1000 genomes]
rs512775	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs514639	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs516080	0.90[ASN][1000 genomes]
rs516620	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs519429	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526990	0.85[ASN][1000 genomes]
rs527928	0.94[ASN][1000 genomes]
rs530293	0.94[ASN][1000 genomes]
rs531331	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.97[ASN][1000 genomes]
rs534604	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs539551	0.98[ASN][1000 genomes]
rs550981	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs552017	0.83[MEX][hapmap]
rs603170	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs680675	0.81[ASN][1000 genomes]
rs7106588	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7110363	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs7111281	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs789599	0.96[ASN][1000 genomes]
rs938728	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs951729	0.84[CHB][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];0.87[ASN][1000 genomes]

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
rs512910	LHX2	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:84967800-85019400	Weak transcription	Ovary	ovary
2	chr11:84994200-85010400	Weak transcription	Psoas Muscle	Psoas
3	chr11:85007000-85007800	Weak transcription	Left Ventricle	heart

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