Variant report

Variant	rs12513939
Chromosome Location	chr5:105577582-105577583
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:105577057..105577825-chr5:106276409..106277049,3	MCF-7	breast:
2	chr5:104952005..104953083-chr5:105576858..105577888,8	MCF-7	breast:
3	chr5:104952188..104952864-chr5:105577091..105577886,5	MCF-7	breast:
4	chr5:104955524..104956144-chr5:105577134..105577974,2	MCF-7	breast:
5	chr5:105576046..105579020-chr5:107007759..107009407,2	MCF-7	breast:
6	chr5:105577109..105578026-chr5:106276409..106277185,3	MCF-7	breast:
7	chr5:105207681..105208221-chr5:105577167..105577841,2	MCF-7	breast:
8	chr5:105457288..105458138-chr5:105577043..105577605,2	MCF-7	breast:
9	chr5:105577079..105577846-chr5:106153949..106154767,2	MCF-7	breast:
10	chr5:104952005..104953083-chr5:105576858..105577888,9	MCF-7	breast:
11	chr5:105577079..105577725-chr5:105702519..105703290,2	MCF-7	breast:
12	chr5:105508454..105509115-chr5:105577016..105577617,2	MCF-7	breast:
13	chr5:105577079..105577587-chr5:106153989..106154803,2	MCF-7	breast:
14	chr5:105525968..105526876-chr5:105576875..105577837,2	MCF-7	breast:
15	chr5:104955261..104956180-chr5:105577014..105577827,4	MCF-7	breast:
16	chr5:103764530..103765315-chr5:105577184..105577701,2	MCF-7	breast:
17	chr5:104952039..104952571-chr5:105577029..105577838,2	MCF-7	breast:

No data

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10037741	0.88[ASN][1000 genomes]
rs10053772	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10054814	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10057027	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10059955	0.85[ASN][1000 genomes]
rs10067178	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10477862	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10477863	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10477864	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11242575	0.90[ASN][1000 genomes]
rs12521315	0.89[ASN][1000 genomes]
rs12655359	0.83[ASN][1000 genomes]
rs12719552	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13167678	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13180375	0.88[ASN][1000 genomes]
rs1369344	0.85[ASN][1000 genomes]
rs1369345	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1435199	0.87[ASN][1000 genomes]
rs1435200	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1865508	0.82[ASN][1000 genomes]
rs1897943	0.87[ASN][1000 genomes]
rs2043502	0.87[ASN][1000 genomes]
rs2082766	0.88[ASN][1000 genomes]
rs35726927	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4260640	0.85[ASN][1000 genomes]
rs4260641	0.85[ASN][1000 genomes]
rs4457046	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4616869	0.91[ASN][1000 genomes]
rs4629569	0.90[ASN][1000 genomes]
rs4958056	0.81[ASN][1000 genomes]
rs57358218	0.81[ASN][1000 genomes]
rs62377601	0.90[ASN][1000 genomes]
rs6859823	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7712613	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7721471	0.90[ASN][1000 genomes]
rs7725559	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7731914	0.88[ASN][1000 genomes]
rs7732235	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7734007	0.89[ASN][1000 genomes]
rs7734465	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9285954	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882655	chr5:105308346-105663646	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv599285	chr5:105355890-106271223	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv882660	chr5:105358229-105685009	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv882666	chr5:105377638-105604520	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	esv2756534	chr5:105427073-105772632	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1028686	chr5:105458958-105624987	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv428123	chr5:105475935-106025350	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv3427509	chr5:105505316-105871362	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv462373	chr5:105507543-105795975	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv599291	chr5:105507543-105795975	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv471036	chr5:105507543-105955784	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:105576800-105577600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:105577000-105577600	Enhancers	A549	lung
3	chr5:105577200-105577600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:105577200-105577600	Enhancers	HepG2	liver
5	chr5:105577400-105577800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links