Variant report

Variant	rs35289288
Chromosome Location	chr3:136680568-136680569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:136675182..136678297-chr3:136678655..136683617,5	K562	blood:
2	chr3:136670696..136673372-chr3:136678994..136680976,2	K562	blood:
3	chr3:136469800..136471530-chr3:136680331..136682096,2	K562	blood:

Variant related genes	Relation type
ENSG00000174564	Chromatin interaction
ENSG00000118007	Chromatin interaction
ENSG00000261758	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10935213	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935214	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1097288	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12054218	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12054219	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12054408	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12494558	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1624703	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1654904	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1654923	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1654925	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1654926	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1682333	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1682337	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1682356	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1682357	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16844325	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16844326	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16844362	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs168635	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2163896	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs361237	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs361239	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs361241	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs361242	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs361243	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs361244	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs361245	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs361246	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs361248	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs361250	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs361251	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs361252	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs747842	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs747843	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs75976	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs75977	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835632	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835633	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs835634	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs835641	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835642	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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	nsv877534	chr3:136676303-136765859	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35289288	PCCB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136656400-136681400	Weak transcription	Fetal Muscle Leg	muscle
2	chr3:136665600-136689400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr3:136675600-136681200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:136677200-136680600	Enhancers	NHDF-Ad	bronchial
5	chr3:136679200-136680600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:136679400-136680600	Enhancers	Muscle Satellite Cultured Cells	--
7	chr3:136679400-136680800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:136679600-136680600	Flanking Active TSS	NHEK	skin
9	chr3:136679600-136681000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:136679800-136680600	Enhancers	NHLF	lung
11	chr3:136680200-136680600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:136680200-136680600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:136680200-136680600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:136680200-136680600	Active TSS	HMEC	breast
15	chr3:136680200-136680800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:136680400-136680800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:136680400-136680800	Weak transcription	HepG2	liver
18	chr3:136680400-136681200	Enhancers	A549	lung
19	chr3:136680400-136682400	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links