Variant report

Variant	rs12426802
Chromosome Location	chr12:106347598-106347599
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:106346252..106348542-chr12:106377078..106379837,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10507207	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10861535	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11112808	0.91[ASN][1000 genomes]
rs11112810	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11112812	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112815	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11608722	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611601	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11837217	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11837987	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12297788	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12425164	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12426791	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12582103	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12810562	0.96[ASN][1000 genomes]
rs12814823	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12815201	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12816747	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818417	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12832619	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12833614	0.95[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1344566	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1344567	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1345543	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1362980	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1362981	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1421454	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1421457	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1421458	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1421459	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1895105	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1895106	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032772	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2080755	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6539238	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6539239	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6539240	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6539241	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6539242	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7300069	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7312545	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7953002	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7953243	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7955474	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7958273	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7960459	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961513	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7965501	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7969437	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7971140	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7971261	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7973513	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973846	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7976523	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9630290	0.95[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.95[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	nsv832508	chr12:106198797-106409112	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12426802	CCDC53	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106339000-106347600	Weak transcription	NHEK	skin
2	chr12:106339200-106348600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:106339200-106348600	Weak transcription	HMEC	breast
4	chr12:106340600-106355800	Weak transcription	Esophagus	oesophagus
5	chr12:106342800-106348800	Weak transcription	HSMMtube	muscle
6	chr12:106343000-106348800	Weak transcription	Aorta	Aorta
7	chr12:106343400-106348600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr12:106346000-106348600	Weak transcription	Left Ventricle	heart
9	chr12:106346000-106348600	Weak transcription	Right Atrium	heart
10	chr12:106346000-106348600	Weak transcription	Right Ventricle	heart
11	chr12:106346200-106348200	Weak transcription	Fetal Heart	heart
12	chr12:106346200-106353800	Weak transcription	Lung	lung
13	chr12:106347400-106349600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:106347400-106349800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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