Variant report

Variant	rs12109506
Chromosome Location	chr5:29148744-29148745
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	TEAD4	chr5:29148702-29149192	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:29145282..29146802-chr5:29147272..29149204,2	MCF-7	breast:
2	chr5:29144206..29145857-chr5:29147427..29149745,2	K562	blood:
3	chr5:29144357..29145929-chr5:29148245..29150453,2	K562	blood:

Variant related genes	Relation type
ENSG00000259786	TF binding region

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10037010	0.81[ASN][1000 genomes]
rs10037061	0.81[ASN][1000 genomes]
rs10038700	0.81[ASN][1000 genomes]
rs10039602	0.81[ASN][1000 genomes]
rs10039668	0.81[ASN][1000 genomes]
rs10039689	0.81[ASN][1000 genomes]
rs10039720	0.81[ASN][1000 genomes]
rs10040911	0.81[ASN][1000 genomes]
rs10042518	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10043330	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10045742	0.81[ASN][1000 genomes]
rs10050492	0.81[ASN][1000 genomes]
rs10056451	0.81[ASN][1000 genomes]
rs10056682	0.81[ASN][1000 genomes]
rs10057831	0.81[ASN][1000 genomes]
rs10057922	0.81[ASN][1000 genomes]
rs10058093	0.81[ASN][1000 genomes]
rs10058226	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10058284	0.81[ASN][1000 genomes]
rs10064605	0.81[ASN][1000 genomes]
rs10064724	0.81[ASN][1000 genomes]
rs10064739	0.81[ASN][1000 genomes]
rs10064857	0.81[ASN][1000 genomes]
rs10064882	0.81[ASN][1000 genomes]
rs10064929	0.81[ASN][1000 genomes]
rs10064947	0.81[ASN][1000 genomes]
rs10065134	0.81[ASN][1000 genomes]
rs10065602	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10066074	0.81[ASN][1000 genomes]
rs10066078	0.81[ASN][1000 genomes]
rs10066277	0.81[ASN][1000 genomes]
rs10068481	0.81[ASN][1000 genomes]
rs10071241	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10072095	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10072535	0.81[ASN][1000 genomes]
rs10072954	0.81[ASN][1000 genomes]
rs10072999	0.81[ASN][1000 genomes]
rs10073201	0.81[ASN][1000 genomes]
rs10074755	0.81[ASN][1000 genomes]
rs10079924	0.81[ASN][1000 genomes]
rs10080202	0.81[ASN][1000 genomes]
rs10440641	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10472145	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10472151	0.81[ASN][1000 genomes]
rs10472154	0.81[ASN][1000 genomes]
rs10472678	0.81[ASN][1000 genomes]
rs10472680	0.81[ASN][1000 genomes]
rs10472681	0.81[ASN][1000 genomes]
rs11742838	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12697209	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13164231	0.81[ASN][1000 genomes]
rs13182294	0.81[ASN][1000 genomes]
rs13356879	0.81[ASN][1000 genomes]
rs13357238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13359197	0.81[ASN][1000 genomes]
rs1478863	0.81[ASN][1000 genomes]
rs1587207	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28637428	0.81[ASN][1000 genomes]
rs309666	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs309670	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34302105	0.81[ASN][1000 genomes]
rs34426391	0.81[ASN][1000 genomes]
rs34687289	0.81[ASN][1000 genomes]
rs34979719	0.81[ASN][1000 genomes]
rs35746880	0.81[ASN][1000 genomes]
rs3853229	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3886358	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4130798	0.81[ASN][1000 genomes]
rs4130799	0.81[ASN][1000 genomes]
rs4130800	0.81[ASN][1000 genomes]
rs4374768	0.81[ASN][1000 genomes]
rs4398647	0.81[ASN][1000 genomes]
rs4631192	0.81[ASN][1000 genomes]
rs55882562	0.92[ASN][1000 genomes]
rs62352828	0.81[ASN][1000 genomes]
rs62352850	0.81[ASN][1000 genomes]
rs62352851	0.81[ASN][1000 genomes]
rs631844	0.89[ASN][1000 genomes]
rs6450669	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6450670	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6450673	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6866060	0.81[ASN][1000 genomes]
rs6873888	0.81[ASN][1000 genomes]
rs6885342	0.81[ASN][1000 genomes]
rs6899088	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7444084	0.81[ASN][1000 genomes]
rs7701404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7714444	0.81[ASN][1000 genomes]
rs7714882	0.81[ASN][1000 genomes]
rs7715935	0.81[ASN][1000 genomes]
rs7722678	0.81[ASN][1000 genomes]
rs7731764	0.81[ASN][1000 genomes]
rs7732750	0.81[ASN][1000 genomes]
rs7732811	0.81[ASN][1000 genomes]
rs7733592	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7737230	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9292297	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9292307	0.81[ASN][1000 genomes]
rs9292311	0.81[ASN][1000 genomes]
rs9292312	0.81[ASN][1000 genomes]
rs9292314	0.81[ASN][1000 genomes]
rs9986176	0.81[ASN][1000 genomes]
rs9986231	0.81[ASN][1000 genomes]
rs9986285	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023990	chr5:28917253-29220447	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	esv3528360	chr5:29069255-29548659	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	esv3528361	chr5:29069255-29548659	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1022253	chr5:29076460-29195987	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1016603	chr5:29102713-29843965	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	nsv537712	chr5:29102713-29843965	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	nsv1030526	chr5:29125802-29204186	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv964827	chr5:29138557-29198352	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:29144000-29150600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:29146800-29150600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:29148000-29151400	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr5:29148400-29149400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:29148600-29149000	Enhancers	H1 Cell Line	embryonic stem cell
6	chr5:29148600-29151400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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