Variant report

Variant	rs9286880
Chromosome Location	chr1:173018680-173018681
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10753070	0.94[ASN][1000 genomes]
rs10912533	0.94[ASN][1000 genomes]
rs11799493	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12034497	0.94[ASN][1000 genomes]
rs2422272	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2901697	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4916297	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4916306	0.94[ASN][1000 genomes]
rs6674831	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831904	chr1:172912110-173070429	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv533953	chr1:172939335-173133255	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9286880	IKZF4	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173013200-173019000	Weak transcription	HSMMtube	muscle
2	chr1:173016000-173018800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr1:173016600-173018800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:173017000-173018800	Enhancers	Primary B cells from cord blood	blood
5	chr1:173017000-173018800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:173017000-173019200	Enhancers	HMEC	breast
7	chr1:173017000-173019200	Enhancers	NHEK	skin
8	chr1:173017200-173018800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:173017200-173018800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:173017200-173018800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:173017200-173020600	Flanking Active TSS	HUVEC	blood vessel
12	chr1:173017400-173018800	Enhancers	NHDF-Ad	bronchial
13	chr1:173017400-173020400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:173017600-173018800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:173017800-173019800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:173018000-173019400	Weak transcription	GM12878-XiMat	blood
17	chr1:173018200-173018800	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr1:173018200-173019800	Weak transcription	A549	lung
19	chr1:173018200-173020000	Weak transcription	NHLF	lung
20	chr1:173018200-173020200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:173018400-173019400	Weak transcription	Fetal Lung	lung
22	chr1:173018400-173019600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:173018400-173019800	Weak transcription	Hela-S3	cervix
24	chr1:173018400-173019800	Weak transcription	NH-A	brain
25	chr1:173018400-173020000	Weak transcription	HSMM	muscle
26	chr1:173018400-173020000	Weak transcription	Osteobl	bone
27	chr1:173018400-173020200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:173018400-173021600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:173018600-173018800	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr1:173018600-173019800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:173018600-173019800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links