Variant report

Variant	rs56120858
Chromosome Location	chr1:222167195-222167196
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11118920	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11118930	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11118931	0.88[EUR][1000 genomes]
rs12031848	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12139468	0.94[EUR][1000 genomes]
rs1339870	0.96[EUR][1000 genomes]
rs1416896	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1470233	0.88[EUR][1000 genomes]
rs2053510	0.88[EUR][1000 genomes]
rs2053511	0.90[EUR][1000 genomes]
rs2053512	0.86[EUR][1000 genomes]
rs2378499	0.94[EUR][1000 genomes]
rs2584314	0.89[EUR][1000 genomes]
rs2584315	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2584316	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2584317	0.89[EUR][1000 genomes]
rs2584318	0.89[EUR][1000 genomes]
rs2584319	0.89[EUR][1000 genomes]
rs2584320	0.88[EUR][1000 genomes]
rs2584321	0.87[EUR][1000 genomes]
rs2584322	0.86[EUR][1000 genomes]
rs2584323	0.89[EUR][1000 genomes]
rs2584324	0.89[EUR][1000 genomes]
rs2584329	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2790744	0.89[EUR][1000 genomes]
rs2790745	0.89[EUR][1000 genomes]
rs2790746	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2790747	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2790748	0.88[EUR][1000 genomes]
rs2800848	0.81[EUR][1000 genomes]
rs2800849	0.88[EUR][1000 genomes]
rs2800861	0.87[EUR][1000 genomes]
rs2800865	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2800866	0.89[EUR][1000 genomes]
rs2800867	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3014719	0.85[EUR][1000 genomes]
rs61823931	0.87[EUR][1000 genomes]
rs6604697	0.87[EUR][1000 genomes]
rs6677832	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7538392	0.89[EUR][1000 genomes]
rs996854	0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014333	chr1:222131785-222245578	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56120858	RP11-815M8.1	cis	lung	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222159600-222169400	Enhancers	HMEC	breast
2	chr1:222162000-222167600	Weak transcription	Brain Substantia Nigra	brain
3	chr1:222163600-222169800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:222164200-222167200	ZNF genes & repeats	GM12878-XiMat	blood
5	chr1:222165000-222167200	Weak transcription	NHDF-Ad	bronchial
6	chr1:222165000-222171600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:222165200-222167200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:222165200-222167200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:222165200-222167200	Weak transcription	NH-A	brain
10	chr1:222165400-222167200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:222165400-222167200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:222165400-222167400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:222165600-222167200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:222165600-222167200	Weak transcription	HSMMtube	muscle
15	chr1:222165600-222167400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:222165600-222167400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:222165800-222172000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:222166400-222168200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:222166600-222167200	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:222166600-222167600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:222166600-222169400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:222166600-222171800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:222166800-222168400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr1:222166800-222169200	Enhancers	Osteobl	bone
25	chr1:222167000-222168200	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr1:222167000-222168200	Enhancers	NHEK	skin
27	chr1:222167000-222168400	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr1:222167000-222169200	Enhancers	HSMM	muscle
29	chr1:222167000-222169200	Enhancers	NHLF	lung
30	chr1:222167000-222169400	Enhancers	Muscle Satellite Cultured Cells	--
31	chr1:222167000-222172000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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