Variant report

Variant	rs2779548
Chromosome Location	chr9:101243852-101243853
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:101242548..101244258-chr9:101471901..101474101,2	MCF-7	breast:
2	chr9:101241326..101244044-chr9:101256381..101258568,2	MCF-7	breast:
3	chr9:101243400..101246141-chr9:101246777..101248511,2	K562	blood:
4	chr9:101243794..101246408-chr9:101558583..101560157,2	MCF-7	breast:
5	chr9:101242211..101245112-chr9:101568714..101571159,2	K562	blood:
6	chr9:101228599..101231536-chr9:101242879..101245760,3	MCF-7	breast:
7	chr9:101243556..101249649-chr9:101264074..101268141,6	MCF-7	breast:
8	chr9:101241642..101243980-chr9:101281362..101284210,2	MCF-7	breast:
9	chr9:101241935..101243986-chr9:101304468..101306501,2	MCF-7	breast:
10	chr9:101230097..101232149-chr9:101241542..101244430,2	K562	blood:
11	chr9:101216040..101217987-chr9:101243398..101245079,2	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2151214	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[ASN][1000 genomes]
rs2779520	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2779532	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2779544	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2779546	0.92[ASN][1000 genomes]
rs2779547	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[ASN][1000 genomes]
rs2779550	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2779552	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2779592	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2779595	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2808542	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2808551	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2808555	0.90[ASN][1000 genomes]
rs2808557	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2808558	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2779548	C9orf3	cis	cerebellum	SCAN
rs2779548	INVS	cis	cerebellum	SCAN
rs2779548	MAGED2	trans	cerebellum	SCAN
rs2779548	HIATL1	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101226400-101248200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr9:101241000-101244200	Weak transcription	Fetal Brain Male	brain
3	chr9:101242200-101245000	Enhancers	NH-A	brain
4	chr9:101242400-101244600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr9:101242400-101245200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr9:101242400-101245200	Enhancers	Osteobl	bone
7	chr9:101242800-101244000	Enhancers	NHEK	skin
8	chr9:101242800-101244400	Enhancers	HMEC	breast
9	chr9:101242800-101244800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr9:101242800-101250000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:101243200-101244400	Enhancers	A549	lung
12	chr9:101243400-101244600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr9:101243600-101244600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:101243800-101244200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:101243800-101244400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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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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