Variant report

Variant	rs7853960
Chromosome Location	chr9:16318055-16318056
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs4961693	0.87[EUR][1000 genomes]
rs7866217	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7870883	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7875643	0.82[EUR][1000 genomes]
rs869625	0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs9406609	0.82[EUR][1000 genomes]
rs9406618	0.93[EUR][1000 genomes]
rs9406619	0.97[EUR][1000 genomes]
rs9407750	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949463	chr9:15970668-16377360	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv429999	chr9:16102066-16389100	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv892644	chr9:16275107-16389006	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv892645	chr9:16292669-16368732	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv613668	chr9:16310620-16377360	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7853960	FREM1	cis	cerebellum	SCAN
rs7853960	TYRP1	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16308800-16318200	Enhancers	Fetal Lung	lung
2	chr9:16312200-16321200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:16314600-16319000	Enhancers	Fetal Muscle Leg	muscle
4	chr9:16315400-16319000	Enhancers	Fetal Stomach	stomach
5	chr9:16315400-16335600	Weak transcription	Right Ventricle	heart
6	chr9:16315800-16318200	Enhancers	Fetal Brain Male	brain
7	chr9:16315800-16319200	Enhancers	Stomach Smooth Muscle	stomach
8	chr9:16315800-16321200	Weak transcription	NHLF	lung
9	chr9:16316000-16321200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr9:16316200-16320600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr9:16316400-16321200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:16316600-16321600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr9:16316800-16318400	Enhancers	Fetal Brain Female	brain
14	chr9:16316800-16319400	Enhancers	Brain Germinal Matrix	brain
15	chr9:16317200-16319200	Enhancers	Brain Anterior Caudate	brain
16	chr9:16317200-16321200	Weak transcription	Adipose Nuclei	Adipose
17	chr9:16317200-16325400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr9:16317600-16320600	Weak transcription	Ovary	ovary
19	chr9:16317600-16321200	Weak transcription	HSMM	muscle
20	chr9:16317800-16318600	Bivalent Enhancer	Brain Substantia Nigra	brain
21	chr9:16318000-16321400	Weak transcription	HSMMtube	muscle

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