Variant report

Variant	rs4300869
Chromosome Location	chr2:179007024-179007025
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr2:179007024-179007344	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
RNU5E-9P	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10176475	0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs10198111	0.82[CHB][hapmap]
rs10432485	0.88[JPT][hapmap]
rs11886139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11887974	0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs11899905	0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs13408924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1347441	0.83[CHB][hapmap]
rs1369515	0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1369517	0.84[ASW][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1435571	0.88[JPT][hapmap];0.91[LWK][hapmap];0.89[YRI][hapmap]
rs2034255	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2163647	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2217838	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs56103916	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6433709	0.82[CHB][hapmap]
rs6709343	0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap]
rs6710329	0.84[ASW][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6714047	0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6738461	0.92[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs6740828	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6754705	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs736842	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs7583491	0.93[CHB][hapmap];0.92[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9288014	0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv875452	chr2:178963445-179167766	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4300869	PLEKHA3	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178978000-179016400	Weak transcription	Gastric	stomach
2	chr2:178987800-179017000	Weak transcription	Fetal Lung	lung
3	chr2:178991000-179009600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:178991200-179007400	Weak transcription	Osteobl	bone
5	chr2:178992400-179007800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:178993200-179016800	Weak transcription	Fetal Intestine Small	intestine
7	chr2:178994400-179007200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:178994400-179007200	Weak transcription	HSMMtube	muscle
9	chr2:178997800-179008200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:179000200-179007200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:179000400-179007200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:179001600-179007200	Weak transcription	HSMM	muscle
13	chr2:179002200-179007200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:179002400-179007800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:179002400-179016800	Weak transcription	Adipose Nuclei	Adipose
16	chr2:179002800-179007200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:179006800-179008000	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr2:179007000-179007200	Enhancers	Fetal Kidney	kidney
19	chr2:179007000-179007400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr2:179007000-179008200	Enhancers	Pancreatic Islets	Pancreatic Islet

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