Variant report

Variant	rs10869809
Chromosome Location	chr9:79347743-79347744
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10735649	0.95[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs10746999	0.81[ASN][1000 genomes]
rs10781372	0.80[AMR][1000 genomes]
rs10781378	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11145045	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17784809	0.84[CHB][hapmap]
rs4744803	0.80[AMR][1000 genomes]
rs670879	0.89[CHB][hapmap]
rs7035263	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7040264	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859406	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7860042	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7868392	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv893481	chr9:79304043-79348193	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10869809	PRUNE2	cis	Whole Blood	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79333200-79359000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:79333200-79370000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr9:79333800-79347800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr9:79340400-79349400	Weak transcription	HSMM	muscle
5	chr9:79341400-79352000	Weak transcription	Brain Hippocampus Middle	brain
6	chr9:79341400-79360800	Weak transcription	Aorta	Aorta
7	chr9:79342600-79347800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr9:79345400-79347800	Weak transcription	HSMMtube	muscle
9	chr9:79346800-79348200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:79347000-79348200	Enhancers	Osteobl	bone
11	chr9:79347200-79348200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:79347200-79348400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:79347200-79348400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:79347400-79347800	Enhancers	Fetal Brain Male	brain
15	chr9:79347400-79348400	Enhancers	Colon Smooth Muscle	Colon
16	chr9:79347600-79348200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:79347600-79349000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr9:79347600-79350600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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Input of quick search could be:

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

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