Variant report

Variant	rs10778889
Chromosome Location	chr12:82739258-82739259
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:82738128..82740375-chr12:82744468..82746353,2	MCF-7	breast:
2	chr12:82738205..82740436-chr12:82743409..82745352,2	MCF-7	breast:
3	chr12:82733369..82734930-chr12:82737197..82739926,2	K562	blood:

Extended variants
information (count: 130 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10506869	1.00[CHB][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10506872	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10506873	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10735453	0.93[ASW][hapmap];1.00[CHB][hapmap];0.97[LWK][hapmap];0.85[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10746241	0.82[AFR][1000 genomes]
rs10746242	1.00[CHB][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10746244	0.93[ASW][hapmap];1.00[CHB][hapmap];0.90[LWK][hapmap];0.89[MKK][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10746245	1.00[CHB][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10778888	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10778895	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10778902	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10778908	1.00[CHB][hapmap]
rs10862480	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10862482	1.00[CHB][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11115234	1.00[ASN][1000 genomes]
rs11115240	1.00[ASN][1000 genomes]
rs11115241	1.00[ASN][1000 genomes]
rs11115242	1.00[ASN][1000 genomes]
rs11831879	1.00[ASN][1000 genomes]
rs11835324	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11836773	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1494023	0.93[ASW][hapmap];1.00[CHB][hapmap];0.90[LWK][hapmap];0.85[MKK][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs1494024	1.00[CHB][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs1494027	1.00[CHB][hapmap]
rs17711838	1.00[ASN][1000 genomes]
rs17712868	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17712927	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17719063	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17719970	1.00[ASN][1000 genomes]
rs17773938	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17774157	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17774489	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17774872	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17775025	1.00[ASN][1000 genomes]
rs17775169	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17776036	1.00[ASN][1000 genomes]
rs17776290	1.00[ASN][1000 genomes]
rs17776375	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2254688	0.80[YRI][hapmap]
rs2401034	0.93[ASW][hapmap];1.00[CHB][hapmap];0.90[LWK][hapmap];0.84[MKK][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2401035	1.00[CHB][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2642010	0.93[ASW][hapmap];1.00[CHB][hapmap];0.90[LWK][hapmap];0.85[MKK][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs2717446	0.93[ASW][hapmap];1.00[CHB][hapmap];0.90[LWK][hapmap];0.84[MKK][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs2731287	1.00[ASN][1000 genomes]
rs2731289	0.85[YRI][hapmap]
rs2731290	0.81[LWK][hapmap]
rs2731291	0.81[LWK][hapmap]
rs2895914	1.00[CHB][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2896434	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34638401	1.00[ASN][1000 genomes]
rs34775923	1.00[ASN][1000 genomes]
rs4143188	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4143189	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4319577	1.00[ASN][1000 genomes]
rs4411333	1.00[CHB][hapmap];0.94[YRI][hapmap];1.00[ASN][1000 genomes]
rs4491327	1.00[ASN][1000 genomes]
rs4495950	0.93[ASW][hapmap];1.00[CHB][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4544081	1.00[CHB][hapmap]
rs4882453	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4882526	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4882527	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4882528	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4882530	1.00[ASN][1000 genomes]
rs57418508	1.00[ASN][1000 genomes]
rs6539659	1.00[ASN][1000 genomes]
rs6539662	1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7138488	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7294780	1.00[ASN][1000 genomes]
rs7294918	1.00[ASN][1000 genomes]
rs7295042	1.00[ASN][1000 genomes]
rs7295566	1.00[ASN][1000 genomes]
rs7304084	1.00[CHB][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7311246	0.93[ASW][hapmap];1.00[CHB][hapmap];0.90[LWK][hapmap];0.85[MKK][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs73149542	1.00[ASN][1000 genomes]
rs73149557	1.00[ASN][1000 genomes]
rs73149567	1.00[ASN][1000 genomes]
rs73149577	1.00[ASN][1000 genomes]
rs73149595	1.00[ASN][1000 genomes]
rs73149597	1.00[ASN][1000 genomes]
rs73151403	1.00[ASN][1000 genomes]
rs73151413	1.00[ASN][1000 genomes]
rs73151422	1.00[ASN][1000 genomes]
rs73151425	1.00[ASN][1000 genomes]
rs73151445	1.00[ASN][1000 genomes]
rs73151447	1.00[ASN][1000 genomes]
rs73151450	1.00[ASN][1000 genomes]
rs73151460	1.00[ASN][1000 genomes]
rs73151484	1.00[ASN][1000 genomes]
rs73151489	1.00[ASN][1000 genomes]
rs73151496	1.00[ASN][1000 genomes]
rs73153504	1.00[ASN][1000 genomes]
rs73153509	1.00[ASN][1000 genomes]
rs73153526	1.00[ASN][1000 genomes]
rs73153530	1.00[ASN][1000 genomes]
rs73153534	1.00[ASN][1000 genomes]
rs73153539	1.00[ASN][1000 genomes]
rs73153551	1.00[ASN][1000 genomes]
rs73153559	1.00[ASN][1000 genomes]
rs73153561	1.00[ASN][1000 genomes]
rs73153569	1.00[ASN][1000 genomes]
rs73153571	1.00[ASN][1000 genomes]
rs73153572	1.00[ASN][1000 genomes]
rs73153573	1.00[ASN][1000 genomes]
rs73153577	1.00[ASN][1000 genomes]
rs73153578	1.00[ASN][1000 genomes]
rs73153584	1.00[ASN][1000 genomes]
rs73153585	1.00[ASN][1000 genomes]
rs73153587	1.00[ASN][1000 genomes]
rs73153588	1.00[ASN][1000 genomes]
rs73153590	1.00[ASN][1000 genomes]
rs73153592	1.00[ASN][1000 genomes]
rs73153599	1.00[ASN][1000 genomes]
rs73155404	1.00[ASN][1000 genomes]
rs73155406	1.00[ASN][1000 genomes]
rs73155441	1.00[ASN][1000 genomes]
rs7488252	0.95[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7956163	1.00[ASN][1000 genomes]
rs7957993	1.00[ASN][1000 genomes]
rs7966041	1.00[ASN][1000 genomes]
rs7967097	1.00[ASN][1000 genomes]
rs7968024	1.00[ASN][1000 genomes]
rs7971746	1.00[ASN][1000 genomes]
rs7977442	0.93[ASW][hapmap];0.86[LWK][hapmap];0.91[MKK][hapmap];0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559539	chr12:82280797-82896218	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1041954	chr12:82314981-83008609	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv541550	chr12:82314981-83008609	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv832471	chr12:82578953-82755360	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1053093	chr12:82645292-83287809	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv541551	chr12:82645292-83287809	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv559541	chr12:82715210-83108395	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10778889	C12orf26	cis	brain	BrainEAC

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:82734800-82742200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr12:82735400-82745200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:82736800-82742200	Weak transcription	Brain Angular Gyrus	brain
4	chr12:82736800-82745000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:82737800-82741200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:82738400-82745200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:82738600-82741200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr12:82739000-82741600	Weak transcription	Primary T cells from cord blood	blood

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