Variant report

Variant	rs12305429
Chromosome Location	chr12:29283282-29283283
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29282290..29284993-chr12:29300811..29302573,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000064763	Chromatin interaction
ENSG00000257258	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10734770	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10743643	0.98[EUR][1000 genomes]
rs11049992	0.86[EUR][1000 genomes]
rs1121577	0.87[EUR][1000 genomes]
rs11502454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12298186	0.86[EUR][1000 genomes]
rs12302010	0.89[EUR][1000 genomes]
rs12302231	0.88[EUR][1000 genomes]
rs12304386	0.89[EUR][1000 genomes]
rs12309591	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12311115	0.92[EUR][1000 genomes]
rs12320204	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12366549	0.86[ASN][1000 genomes]
rs1353460	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1390542	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1496221	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17449204	0.85[EUR][1000 genomes]
rs17449238	0.85[EUR][1000 genomes]
rs1826801	0.85[EUR][1000 genomes]
rs1865763	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1865764	0.97[EUR][1000 genomes]
rs2164493	1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[EUR][1000 genomes]
rs2196479	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2349971	1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28544897	0.92[EUR][1000 genomes]
rs3940535	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4930849	0.97[EUR][1000 genomes]
rs4930850	0.86[EUR][1000 genomes]
rs4931154	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59113616	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60329521	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6487757	0.97[EUR][1000 genomes]
rs6487764	0.91[EUR][1000 genomes]
rs66487137	0.89[EUR][1000 genomes]
rs66712682	0.89[EUR][1000 genomes]
rs67060812	0.89[EUR][1000 genomes]
rs67087836	0.89[EUR][1000 genomes]
rs67287552	0.89[EUR][1000 genomes]
rs67563394	0.89[EUR][1000 genomes]
rs67760969	0.92[EUR][1000 genomes]
rs716704	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7304088	0.97[EUR][1000 genomes]
rs73061737	0.89[EUR][1000 genomes]
rs73061745	0.89[EUR][1000 genomes]
rs7315912	0.97[EUR][1000 genomes]
rs7316030	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73254758	0.92[EUR][1000 genomes]
rs73254786	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73268857	0.85[EUR][1000 genomes]
rs73268858	0.85[EUR][1000 genomes]
rs73273123	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7964313	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7966290	1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[EUR][1000 genomes]
rs7966398	1.00[JPT][hapmap];0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	esv2758301	chr12:29110782-29289849	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2759888	chr12:29110782-29289849	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12305429	RP11-996F15.2	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29266400-29286400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:29283000-29283400	Enhancers	Dnd41	blood
3	chr12:29283000-29284400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links