Variant report

Variant	rs10512860
Chromosome Location	chr5:44539953-44539954
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:44538904..44540279-chr5:44568353..44569227,4	MCF-7	breast:
2	chr5:44538575..44540262-chr5:44568240..44569247,12	MCF-7	breast:
3	chr5:44539237..44540214-chr5:44568240..44569147,5	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10054521	0.90[ASN][1000 genomes]
rs10066953	0.85[ASN][1000 genomes]
rs10070248	0.85[ASN][1000 genomes]
rs10079222	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12374507	0.85[ASN][1000 genomes]
rs12516346	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13182481	0.92[ASN][1000 genomes]
rs1351633	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1384453	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1384454	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1482663	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1482665	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1482684	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1482690	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1482691	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1905191	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1905192	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34787390	0.83[ASN][1000 genomes]
rs4352602	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4463187	0.92[ASN][1000 genomes]
rs4485936	0.87[ASN][1000 genomes]
rs4529201	0.87[ASN][1000 genomes]
rs4866776	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4866899	0.94[EUR][1000 genomes]
rs4866905	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58761628	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6451763	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6864776	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6879342	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6897963	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7703171	0.91[EUR][1000 genomes]
rs7707044	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7710996	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7712213	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7736427	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9654396	0.85[ASN][1000 genomes]
rs983940	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv830277	chr5:44383402-44566881	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10512860	PLCXD3	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:44528200-44544800	Weak transcription	Fetal Lung	lung
2	chr5:44538800-44540000	Flanking Active TSS	Hela-S3	cervix
3	chr5:44539000-44540000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
4	chr5:44539000-44540000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr5:44539200-44540000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:44539200-44540000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:44539400-44540000	Enhancers	Fetal Muscle Leg	muscle
8	chr5:44539600-44540000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:44539600-44540000	Enhancers	Psoas Muscle	Psoas
10	chr5:44539800-44540000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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