Variant report

Variant	rs12046297
Chromosome Location	chr1:224043982-224043983
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	chr1:224042155..224044743-chr1:224047523..224049219,2	MCF-7	breast:
2	chr1:224031495..224036851-chr1:224037356..224045519,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10159015	0.90[ASN][1000 genomes]
rs10503144	0.91[EUR][1000 genomes]
rs1153965	0.82[EUR][1000 genomes]
rs12022914	0.83[ASN][1000 genomes]
rs12022920	0.83[ASN][1000 genomes]
rs12024059	0.83[ASN][1000 genomes]
rs12028843	0.83[ASN][1000 genomes]
rs12031859	0.83[ASN][1000 genomes]
rs12034120	0.85[ASN][1000 genomes]
rs12034914	0.85[ASN][1000 genomes]
rs12036717	0.85[ASN][1000 genomes]
rs12038665	0.83[ASN][1000 genomes]
rs12038706	0.85[ASN][1000 genomes]
rs12039721	0.85[ASN][1000 genomes]
rs12040996	0.85[ASN][1000 genomes]
rs12044652	0.85[ASN][1000 genomes]
rs12044659	0.85[ASN][1000 genomes]
rs12047342	0.85[ASN][1000 genomes]
rs12059128	0.89[EUR][1000 genomes]
rs12059770	0.89[EUR][1000 genomes]
rs12060361	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12080250	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12088254	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12091841	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12563477	0.86[EUR][1000 genomes]
rs12565967	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12566817	0.91[EUR][1000 genomes]
rs16842162	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16842229	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16842257	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16842259	0.83[ASN][1000 genomes]
rs16842326	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs28370073	0.83[EUR][1000 genomes]
rs28370074	0.83[EUR][1000 genomes]
rs28370088	0.88[EUR][1000 genomes]
rs28370159	0.82[EUR][1000 genomes]
rs28370160	0.81[ASN][1000 genomes]
rs28370170	0.86[EUR][1000 genomes]
rs34683843	0.89[EUR][1000 genomes]
rs36032024	0.91[EUR][1000 genomes]
rs3885657	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61437308	0.83[ASN][1000 genomes]
rs61823580	0.91[EUR][1000 genomes]
rs61823581	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61823583	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61823585	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61823587	0.91[EUR][1000 genomes]
rs61823591	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61824003	0.86[EUR][1000 genomes]
rs61824005	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61824008	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6604724	0.89[EUR][1000 genomes]
rs6604727	0.91[EUR][1000 genomes]
rs6604728	0.93[EUR][1000 genomes]
rs6604729	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6604730	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6658954	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6678365	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6682964	0.89[EUR][1000 genomes]
rs6685557	0.89[EUR][1000 genomes]
rs6691315	0.89[EUR][1000 genomes]
rs6694960	0.89[EUR][1000 genomes]
rs6700366	0.90[EUR][1000 genomes]
rs7331	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7528455	0.93[EUR][1000 genomes]
rs7530328	0.89[EUR][1000 genomes]
rs7533551	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7535882	0.90[EUR][1000 genomes]
rs7552702	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv945311	chr1:224043754-224046221	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224041800-224047000	Weak transcription	NHEK	skin
2	chr1:224041800-224047200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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