Variant report

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10005042	0.84[EUR][1000 genomes]
rs10007169	0.90[ASN][1000 genomes]
rs10010642	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10029180	0.88[EUR][1000 genomes]
rs10518355	0.86[EUR][1000 genomes]
rs13434556	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13435523	0.91[ASN][1000 genomes]
rs1396533	0.85[EUR][1000 genomes]
rs1526324	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1554730	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17013770	0.91[ASN][1000 genomes]
rs17013889	0.91[ASN][1000 genomes]
rs17013907	0.91[ASN][1000 genomes]
rs17013908	0.91[ASN][1000 genomes]
rs17315319	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28446046	0.88[EUR][1000 genomes]
rs28472543	0.80[EUR][1000 genomes]
rs28503893	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28624642	0.87[EUR][1000 genomes]
rs28634547	0.95[EUR][1000 genomes]
rs28749277	0.88[EUR][1000 genomes]
rs6534179	0.89[EUR][1000 genomes]
rs6856851	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6856905	0.83[AMR][1000 genomes];0.95[EUR][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	nsv1007641	chr4:120884220-121555889	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv537234	chr4:120884220-121555889	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv595333	chr4:121093248-121440368	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1005240	chr4:121093285-121420997	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv879852	chr4:121108734-121768496	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9991289	SYNPO2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:121252400-121254600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:121252600-121253600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:121252600-121253800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:121252800-121253600	Enhancers	Brain Germinal Matrix	brain
5	chr4:121252800-121254000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr4:121253000-121253800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:121253200-121253600	Enhancers	NHDF-Ad	bronchial

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