Variant report

Variant	rs12513447
Chromosome Location	chr5:75370737-75370738
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr5:75370373-75370768	HCT-116	colon:	n/a	chr5:75370691-75370700 chr5:75370511-75370530
2	CTCF	chr5:75370294-75370817	MCF-7	breast:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
3	RAD21	chr5:75370242-75370758	HCT-116	colon:	n/a	chr5:75370691-75370700 chr5:75370511-75370530
4	RAD21	chr5:75370386-75370751	A549	lung:	n/a	chr5:75370691-75370700 chr5:75370511-75370530
5	RAD21	chr5:75370270-75370755	MCF-7	breast:	n/a	chr5:75370691-75370700 chr5:75370511-75370530
6	SMC3	chr5:75370312-75370744	GM12878	blood:	n/a	chr5:75370512-75370519
7	RAD21	chr5:75370285-75370781	H1-hESC	embryonic stem cell:	n/a	chr5:75370691-75370700 chr5:75370511-75370530
8	RAD21	chr5:75370390-75370791	ECC-1	luminal epithelium:	n/a	chr5:75370691-75370700 chr5:75370511-75370530
9	RAD21	chr5:75370163-75370896	SK-N-SH	brain:	n/a	chr5:75370691-75370700 chr5:75370511-75370530
10	RAD21	chr5:75370290-75370762	A549	lung:	n/a	chr5:75370691-75370700 chr5:75370511-75370530
11	RAD21	chr5:75370300-75370744	MCF-7	breast:	n/a	chr5:75370691-75370700 chr5:75370511-75370530
12	CTCF	chr5:75370411-75370790	HCT-116	colon:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
13	FOXM1	chr5:75370260-75370857	GM12878	blood:	n/a	n/a
14	CTCF	chr5:75370720-75370870	HAc	cerebellar:	n/a	n/a
15	RAD21	chr5:75370324-75370816	H1-hESC	embryonic stem cell:	n/a	chr5:75370691-75370700 chr5:75370511-75370530
16	SMC3	chr5:75370206-75370952	SK-N-SH	brain:	n/a	chr5:75370512-75370519
17	CTCF	chr5:75370184-75370816	SK-N-SH	brain:	n/a	chr5:75370513-75370522 chr5:75370512-75370533

No.	Distal block	Cell Line	Cell type
1	chr5:75370241..75371009-chr5:75551554..75552357,4	K562	blood:
2	chr5:75370056..75370744-chr5:75551849..75552754,4	MCF-7	breast:
3	chr5:75370258..75370917-chr5:75470691..75471438,2	MCF-7	breast:
4	chr5:75370186..75371274-chr5:75551816..75552790,4	MCF-7	breast:
5	chr5:75370002..75370997-chr5:75470399..75471572,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251342	TF binding region
ENSG00000249777	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10038280	0.89[EUR][1000 genomes]
rs10038757	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10043369	0.90[EUR][1000 genomes]
rs10050813	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10054931	0.90[EUR][1000 genomes]
rs10063621	0.92[EUR][1000 genomes]
rs10064145	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10065114	0.91[EUR][1000 genomes]
rs10474460	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12513411	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12656979	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1553311	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17673786	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17746749	0.91[EUR][1000 genomes]
rs1862520	0.91[EUR][1000 genomes]
rs28554027	0.95[EUR][1000 genomes]
rs6453199	0.89[EUR][1000 genomes]
rs7448740	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs767590	0.91[EUR][1000 genomes]
rs7700761	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7702044	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7711218	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7712198	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7725280	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9293666	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9293667	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv4883	chr5:75360926-75373963	Weak transcription Bivalent Enhancer Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
4	nsv869885	chr5:75365786-75419656	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1033350	chr5:75367809-75538460	Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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