Variant report

Variant	rs2078415
Chromosome Location	chr6:48395074-48395075
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1013401	0.87[EUR][1000 genomes]
rs10456584	0.83[EUR][1000 genomes]
rs12202558	0.85[EUR][1000 genomes]
rs12664774	0.90[EUR][1000 genomes]
rs1348411	0.90[EUR][1000 genomes]
rs1373189	0.81[EUR][1000 genomes]
rs1373191	0.81[EUR][1000 genomes]
rs1582092	0.87[EUR][1000 genomes]
rs1582093	0.87[EUR][1000 genomes]
rs17289609	0.85[EUR][1000 genomes]
rs2396863	0.90[EUR][1000 genomes]
rs2396865	0.90[EUR][1000 genomes]
rs2586826	0.85[EUR][1000 genomes]
rs2586827	0.87[EUR][1000 genomes]
rs2798765	0.81[EUR][1000 genomes]
rs2996265	0.85[EUR][1000 genomes]
rs2996266	0.85[EUR][1000 genomes]
rs2996267	0.84[EUR][1000 genomes]
rs34367220	0.91[EUR][1000 genomes]
rs6927980	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9463405	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9473361	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9473384	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv603035	chr6:47902243-48700995	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1033151	chr6:48067287-48797029	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv538217	chr6:48067287-48797029	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv885877	chr6:48117685-48626930	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv917050	chr6:48168742-48578496	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv830657	chr6:48387714-48566656	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2078415	SSFA2	trans	cerebellum	SCAN
rs2078415	RORC	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:48392200-48396800	Weak transcription	NH-A	brain
2	chr6:48393200-48395600	Enhancers	HMEC	breast
3	chr6:48393200-48398800	Enhancers	NHLF	lung
4	chr6:48393800-48395200	Enhancers	HSMM	muscle
5	chr6:48393800-48395400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:48393800-48398800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:48393800-48399000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:48394000-48395600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:48394200-48395600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:48394200-48395800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:48394400-48395200	Enhancers	Osteobl	bone
12	chr6:48394400-48395800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:48394800-48395200	Enhancers	NHDF-Ad	bronchial
14	chr6:48394800-48396800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:48394800-48396800	Weak transcription	NHEK	skin
16	chr6:48394800-48397000	Weak transcription	HUVEC	blood vessel
17	chr6:48394800-48397200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:48395000-48399000	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links