Variant report

Variant	rs12202744
Chromosome Location	chr6:72244301-72244302
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:72243298..72244696-chr6:72794179..72795337,7	MCF-7	breast:
2	chr6:72243672..72245275-chr6:72792459..72794450,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10455236	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10805938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942950	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1156360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12195280	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12196715	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12196908	0.81[EUR][1000 genomes]
rs12198869	0.84[AFR][1000 genomes]
rs12198962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12202510	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12202768	0.85[EUR][1000 genomes]
rs12204199	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12204236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12204508	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12205019	0.85[EUR][1000 genomes]
rs12206174	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12206434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12207845	0.85[EUR][1000 genomes]
rs12208819	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12210244	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12213508	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12214509	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12524965	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12525003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528422	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13204740	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1527712	0.83[EUR][1000 genomes]
rs1814045	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs199625	0.89[ASN][1000 genomes]
rs2129327	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62404028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62404029	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62404039	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922155	0.81[EUR][1000 genomes]
rs9358958	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830684	chr6:72094842-72282684	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	488 gene(s)	inside rSNPs	diseases
2	nsv830685	chr6:72244007-72410757	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12202744	P2RX3	trans	cerebellum	SCAN
rs12202744	LMBRD1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:72241800-72244600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:72244000-72245000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:72244000-72245600	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links