Variant report

Variant	rs12478760
Chromosome Location	chr2:179185051-179185052
allele	A/G
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	POLR2A	chr2:179185046-179185135	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
OSBPL6	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10497513	0.86[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10497514	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10930829	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs12151447	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12464380	0.93[GIH][hapmap];0.80[TSI][hapmap]
rs12464536	0.97[ASN][1000 genomes]
rs12464806	0.92[GIH][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs12467040	0.81[EUR][1000 genomes]
rs12467053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12471790	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12473890	0.88[EUR][1000 genomes]
rs12474802	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs12474844	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs12474919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12478837	0.81[EUR][1000 genomes]
rs12479027	0.87[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs12479281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12618595	0.87[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs12618660	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12620577	0.95[ASN][1000 genomes]
rs12620729	0.95[ASN][1000 genomes]
rs13402976	0.93[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs1368905	0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs1434082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1434083	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1434084	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs1434086	0.97[ASN][1000 genomes]
rs1434089	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs16866256	0.97[ASN][1000 genomes]
rs16866271	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs16866272	0.84[EUR][1000 genomes]
rs16866273	0.93[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs16866275	0.93[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs16866281	0.93[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs16866299	0.81[JPT][hapmap]
rs1812550	0.86[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1836203	0.84[ASN][1000 genomes]
rs1982104	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3813252	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs3813253	0.87[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs4422196	0.84[ASN][1000 genomes]
rs4894008	0.83[EUR][1000 genomes]
rs4894009	0.82[EUR][1000 genomes]
rs4894011	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4894012	0.91[EUR][1000 genomes]
rs4894013	0.93[GIH][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs4894014	0.84[ASN][1000 genomes]
rs55989867	0.85[ASN][1000 genomes]
rs56148541	0.97[ASN][1000 genomes]
rs56366027	0.85[ASN][1000 genomes]
rs6433722	0.86[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6718010	0.81[EUR][1000 genomes]
rs6754517	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6760059	0.92[GIH][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs6761421	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs718650	0.94[ASN][1000 genomes]
rs718651	0.95[ASN][1000 genomes]
rs73032568	0.88[EUR][1000 genomes]
rs7559699	0.84[ASN][1000 genomes]
rs7559711	0.84[ASN][1000 genomes]
rs7572355	0.82[ASN][1000 genomes]
rs7576065	0.81[EUR][1000 genomes]
rs7576231	0.81[EUR][1000 genomes]
rs7587155	0.81[EUR][1000 genomes]
rs964165	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs9646740	0.85[EUR][1000 genomes]

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	nsv834466	chr2:179140792-179284778	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12478760	PLEKHA3	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179143200-179188600	Weak transcription	Brain Anterior Caudate	brain
2	chr2:179160200-179188600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:179164600-179200800	Weak transcription	Aorta	Aorta
4	chr2:179176200-179198000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:179181000-179188600	Weak transcription	K562	blood
6	chr2:179182400-179185400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:179183800-179187400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr2:179183800-179188800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:179183800-179192600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:179183800-179247800	Weak transcription	Psoas Muscle	Psoas
11	chr2:179184400-179186000	Enhancers	Liver	Liver
12	chr2:179184600-179185400	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr2:179184600-179188400	Weak transcription	Fetal Brain Male	brain
14	chr2:179184800-179185200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:179184800-179185400	Enhancers	Fetal Lung	lung
16	chr2:179184800-179185600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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