Variant report

Variant	rs12430260
Chromosome Location	chr13:54782065-54782066
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	chr13:54780172..54782257-chr13:54783482..54785302,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs12427903	0.92[EUR][1000 genomes]
rs12429828	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12429973	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1577577	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17089302	0.88[AFR][1000 genomes]
rs17089308	0.88[AFR][1000 genomes]
rs17089310	0.88[AFR][1000 genomes]
rs17604306	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17667588	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17667614	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1855847	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1889824	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1960782	0.89[EUR][1000 genomes]
rs1984140	0.89[EUR][1000 genomes]
rs1984141	0.89[EUR][1000 genomes]
rs2050378	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2065822	0.89[EUR][1000 genomes]
rs2152084	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2576122	0.89[EUR][1000 genomes]
rs2576124	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2576125	0.89[EUR][1000 genomes]
rs2576126	0.89[EUR][1000 genomes]
rs2576127	0.89[EUR][1000 genomes]
rs2576128	0.87[EUR][1000 genomes]
rs2576129	0.89[EUR][1000 genomes]
rs2576131	0.89[EUR][1000 genomes]
rs2576135	0.81[EUR][1000 genomes]
rs2576136	0.89[EUR][1000 genomes]
rs2576147	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs2782502	0.86[ASN][1000 genomes]
rs2784555	0.84[EUR][1000 genomes]
rs2784556	0.83[EUR][1000 genomes]
rs2784559	0.86[EUR][1000 genomes]
rs2784560	0.89[EUR][1000 genomes]
rs2784561	0.89[EUR][1000 genomes]
rs2784562	0.89[EUR][1000 genomes]
rs2784564	0.89[EUR][1000 genomes]
rs2784566	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2784567	0.85[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2784568	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2784569	0.82[EUR][1000 genomes]
rs2784572	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2818222	0.86[ASN][1000 genomes]
rs2818223	0.86[ASN][1000 genomes]
rs2818224	0.86[ASN][1000 genomes]
rs4883886	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4883887	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4884928	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57804893	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58112675	0.84[AFR][1000 genomes]
rs60572618	0.84[AFR][1000 genomes]
rs682930	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684299	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs795647	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs795649	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs878942	0.89[EUR][1000 genomes]
rs933101	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs988527	0.89[EUR][1000 genomes]
rs988528	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3375545	chr13:54517432-54908108	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv561701	chr13:54711276-54826104	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1051063	chr13:54777487-54997866	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
4	nsv541778	chr13:54777487-54997866	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:54775600-54784600	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr13:54780200-54782200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr13:54780800-54782400	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr13:54781000-54782400	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr13:54781000-54783600	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr13:54781600-54784800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr13:54781800-54784600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr13:54782000-54784600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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