Variant report

Variant	rs12494462
Chromosome Location	chr3:51541171-51541172
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:51421519..51423877-chr3:51540078..51542702,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145050	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10510757	0.88[ASN][1000 genomes]
rs10510758	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12485610	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486568	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12487426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487468	0.89[ASN][1000 genomes]
rs12489414	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12490471	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490889	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12491048	0.92[ASN][1000 genomes]
rs12492624	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493265	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12493618	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12493857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493978	0.89[ASN][1000 genomes]
rs12494979	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12496340	0.93[EUR][1000 genomes]
rs13089799	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13090348	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13324384	0.87[EUR][1000 genomes]
rs1370124	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17051783	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17051811	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17661242	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17712228	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1842394	0.81[ASN][1000 genomes]
rs2033703	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2082992	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2082993	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2217938	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2241785	0.92[ASN][1000 genomes]
rs2304512	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2306430	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2306431	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2356261	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2356298	1.00[ASN][1000 genomes]
rs35536327	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3749317	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3792408	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3804766	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3828395	0.91[ASN][1000 genomes]
rs4468966	0.84[ASN][1000 genomes]
rs4687553	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4687563	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4687592	0.81[EUR][1000 genomes]
rs4687599	0.87[EUR][1000 genomes]
rs4687601	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4687605	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687610	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4687656	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687691	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687731	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4687769	0.87[EUR][1000 genomes]
rs4687777	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4687794	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687803	0.90[AMR][1000 genomes]
rs4687804	0.83[AMR][1000 genomes]
rs4687811	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4687812	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4687813	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4974096	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs55667499	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55671465	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs55706150	0.87[EUR][1000 genomes]
rs55872019	0.81[EUR][1000 genomes]
rs56239081	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56729479	1.00[ASN][1000 genomes]
rs57027950	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57047724	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs57603251	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs57700326	0.81[ASN][1000 genomes]
rs57831708	0.92[ASN][1000 genomes]
rs58059174	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58189274	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58201844	0.84[ASN][1000 genomes]
rs58568178	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs58762652	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58836277	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59563413	0.88[ASN][1000 genomes]
rs59564034	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59838596	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59953568	0.89[ASN][1000 genomes]
rs60007226	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60606339	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61233013	0.97[ASN][1000 genomes]
rs61419317	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61689323	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72945708	0.88[ASN][1000 genomes]
rs72945713	0.92[ASN][1000 genomes]
rs72951443	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72951490	0.87[EUR][1000 genomes]
rs7375146	0.87[EUR][1000 genomes]
rs73834252	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73834253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73834254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73834258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73834265	0.87[EUR][1000 genomes]
rs73837439	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73837442	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73837443	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs751076	0.84[ASN][1000 genomes]
rs7642698	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs880478	0.84[ASN][1000 genomes]
rs9817077	0.83[ASN][1000 genomes]
rs9817872	0.83[ASN][1000 genomes]
rs9819195	0.83[ASN][1000 genomes]
rs9820140	0.92[ASN][1000 genomes]
rs9827186	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9829057	0.84[ASN][1000 genomes]
rs9842600	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9843583	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9856134	0.83[ASN][1000 genomes]
rs9861019	0.91[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	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51535000-51541400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:51536400-51543200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr3:51537000-51543800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:51538000-51543400	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links