Variant report

Variant	rs12467053
Chromosome Location	chr2:179192070-179192071
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:179186226..179189549-chr2:179191387..179194072,3	K562	blood:
2	chr2:179183577..179186418-chr2:179191406..179193848,2	MCF-7	breast:
3	chr2:179192053..179195565-chr2:179199855..179202518,3	K562	blood:

Variant related genes	Relation type
ENSG00000079156	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

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];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12464380	0.86[GIH][hapmap];0.89[MKK][hapmap];0.80[TSI][hapmap]
rs12464536	0.97[ASN][1000 genomes]
rs12464806	0.86[GIH][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12467040	0.83[EUR][1000 genomes]
rs12471790	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12473890	0.87[AFR][1000 genomes];0.91[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];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12478760	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]
rs12478837	0.88[YRI][hapmap];0.83[EUR][1000 genomes]
rs12479027	0.87[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs12479281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	0.96[ASN][1000 genomes]
rs12620729	0.96[ASN][1000 genomes]
rs13402976	0.86[GIH][hapmap];0.88[TSI][hapmap];0.88[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];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1434083	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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	0.98[ASN][1000 genomes]
rs16866271	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs16866272	0.87[EUR][1000 genomes]
rs16866273	0.93[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs16866275	0.93[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs16866281	0.93[CHB][hapmap];0.95[JPT][hapmap];0.96[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];0.97[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];0.86[ASN][1000 genomes]
rs4422196	0.84[ASN][1000 genomes]
rs4894008	0.81[EUR][1000 genomes]
rs4894011	0.87[ASN][1000 genomes]
rs4894012	0.88[EUR][1000 genomes]
rs4894013	0.86[GIH][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs4894014	0.84[ASN][1000 genomes]
rs55989867	0.85[ASN][1000 genomes]
rs56148541	0.97[ASN][1000 genomes]
rs56366027	0.86[ASN][1000 genomes]
rs6433722	0.86[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6718010	0.83[EUR][1000 genomes]
rs6754517	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6760059	0.86[GIH][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs6761421	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs718650	0.95[ASN][1000 genomes]
rs718651	0.96[ASN][1000 genomes]
rs73032568	0.91[EUR][1000 genomes]
rs7559699	0.84[ASN][1000 genomes]
rs7559711	0.84[ASN][1000 genomes]
rs7572355	0.83[ASN][1000 genomes]
rs7576065	0.88[YRI][hapmap];0.83[EUR][1000 genomes]
rs7576231	0.88[YRI][hapmap];0.83[EUR][1000 genomes]
rs7587155	0.83[EUR][1000 genomes]
rs964165	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs9646740	0.88[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
rs12467053	PLEKHA3	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179164600-179200800	Weak transcription	Aorta	Aorta
2	chr2:179176200-179198000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:179183800-179192600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:179183800-179247800	Weak transcription	Psoas Muscle	Psoas
5	chr2:179185400-179198200	Weak transcription	Fetal Lung	lung
6	chr2:179186000-179195000	Weak transcription	Liver	Liver
7	chr2:179188800-179195000	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:179189000-179192400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:179189000-179193400	Weak transcription	K562	blood
10	chr2:179189200-179196800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr2:179189200-179201200	Weak transcription	Ovary	ovary
12	chr2:179189400-179201200	Weak transcription	Fetal Brain Male	brain
13	chr2:179189800-179217000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:179190600-179192200	Enhancers	HSMMtube	muscle
15	chr2:179190600-179195800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:179191800-179194000	Enhancers	HSMM	muscle
17	chr2:179192000-179193200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:179192000-179193600	Enhancers	Muscle Satellite Cultured Cells	--

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