Variant report

Variant	rs2779552
Chromosome Location	chr9:101254476-101254477
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17770838	0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs2151214	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2779520	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2779532	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2779544	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2779546	0.91[ASN][1000 genomes]
rs2779547	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2779548	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2779550	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2779592	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2779595	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2808542	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2808551	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2808555	0.83[ASN][1000 genomes]
rs2808557	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2808558	0.90[CHB][hapmap];1.00[JPT][hapmap];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	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv831665	chr9:101170061-101367692	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv6630	chr9:101236324-101267349	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2779552	C9orf3	cis	cerebellum	SCAN
rs2779552	HIATL1	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101247000-101263800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr9:101248400-101264200	Weak transcription	Brain Angular Gyrus	brain
3	chr9:101248800-101264200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr9:101250000-101255000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:101250800-101254600	Enhancers	Muscle Satellite Cultured Cells	--
6	chr9:101251400-101255600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr9:101251600-101258400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr9:101251600-101263800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr9:101252600-101254600	Enhancers	Osteobl	bone
10	chr9:101252800-101254600	Enhancers	Liver	Liver
11	chr9:101253000-101254600	Enhancers	NH-A	brain
12	chr9:101253200-101255200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:101253400-101254600	Enhancers	Fetal Heart	heart
14	chr9:101253400-101254600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr9:101254000-101255600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr9:101254000-101257400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:101254400-101256200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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