Variant report

Variant	rs7839902
Chromosome Location	chr8:10915209-10915210
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10096332	0.91[CEU][hapmap];0.91[CHB][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs10111974	0.90[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs11250113	0.84[CHB][hapmap]
rs11775350	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12115017	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13251510	0.87[ASN][1000 genomes]
rs28447601	0.81[ASN][1000 genomes]
rs56078888	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6601552	0.91[CEU][hapmap];0.82[CHB][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6601553	0.84[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6601554	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6983301	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6993779	0.81[CEU][hapmap];0.83[CHB][hapmap];0.81[EUR][1000 genomes]
rs6997523	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7016414	0.88[ASN][1000 genomes]
rs7016760	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7462014	0.91[CHB][hapmap]
rs7815958	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7821584	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

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	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1022434	chr8:10866242-10916523	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7839902	SNORD45A	trans	cerebellum	SCAN
rs7839902	DEFB136	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10907400-10916200	Weak transcription	Brain Germinal Matrix	brain
2	chr8:10911200-10916400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr8:10911600-10916200	Weak transcription	Brain Anterior Caudate	brain
4	chr8:10911600-10916400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr8:10912600-10916400	Weak transcription	HSMMtube	muscle
6	chr8:10913600-10916600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr8:10913600-10916600	Weak transcription	Lung	lung
8	chr8:10914800-10915400	Enhancers	Brain Cingulate Gyrus	brain
9	chr8:10915000-10916200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr8:10915200-10916400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr8:10915200-10916400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr8:10915200-10916600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr8:10915200-10916600	Weak transcription	Gastric	stomach

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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