Variant report

Variant	rs7939524
Chromosome Location	chr11:120807571-120807572
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr11:120807559-120807890	SH-SY5Y	brain:	n/a	chr11:120807676-120807684

Variant related genes	Relation type
HMGB1P42	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10892647	0.95[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs10892648	0.95[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10892651	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11218066	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11218068	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11218069	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11218070	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11218071	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11218072	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11218074	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11218075	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11218080	0.86[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs12361041	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12419730	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17124570	0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs17124575	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2186621	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35024210	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3781816	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3781817	0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs4935757	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4936565	0.90[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4936566	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4936568	0.90[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs7113018	0.90[CHB][hapmap]
rs73007850	0.88[ASN][1000 genomes]
rs73007893	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73007896	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7926317	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1042469	chr11:120799275-120846585	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv541183	chr11:120799275-120846585	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120800200-120808200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr11:120800400-120808400	Weak transcription	Brain Anterior Caudate	brain
3	chr11:120800600-120815200	Weak transcription	Brain Hippocampus Middle	brain
4	chr11:120801000-120811400	Weak transcription	Fetal Lung	lung
5	chr11:120802200-120823200	Weak transcription	Ovary	ovary
6	chr11:120803600-120808400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr11:120805400-120809200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr11:120805400-120809800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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