Variant report

Variant	rs17860502
Chromosome Location	chr5:147466001-147466002
allele	A/G
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	RCOR1	chr5:147465513-147466148	Hela-S3	cervix:	n/a	n/a
2	RFX5	chr5:147465372-147466180	Hela-S3	cervix:	n/a	n/a
3	EP300	chr5:147465529-147466064	Hela-S3	cervix:	n/a	n/a
4	E2F4	chr5:147465954-147466034	MCF10A-Er-Src	breast:	n/a	n/a
5	BRCA1	chr5:147465542-147466030	Hela-S3	cervix:	n/a	n/a
6	TCF7L2	chr5:147465560-147466087	Hela-S3	cervix:	n/a	chr5:147465906-147465922

Variant related genes	Relation type
SPINK5	TF binding region

Extended variants
information (count: 108 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10074782	0.81[EUR][1000 genomes]
rs10491340	1.00[AFR][1000 genomes]
rs10491341	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10491342	0.81[EUR][1000 genomes]
rs11948836	0.81[EUR][1000 genomes]
rs11950029	0.84[EUR][1000 genomes]
rs11951613	0.84[EUR][1000 genomes]
rs11951614	0.84[EUR][1000 genomes]
rs11952442	0.84[EUR][1000 genomes]
rs11954011	0.84[EUR][1000 genomes]
rs11955612	0.84[EUR][1000 genomes]
rs11956309	0.84[EUR][1000 genomes]
rs11957191	0.84[EUR][1000 genomes]
rs11957744	0.84[EUR][1000 genomes]
rs11958071	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11958866	0.84[EUR][1000 genomes]
rs11960620	0.84[EUR][1000 genomes]
rs12332673	0.81[EUR][1000 genomes]
rs1363718	0.84[EUR][1000 genomes]
rs1363719	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1363720	0.84[EUR][1000 genomes]
rs1422985	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1422986	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17107575	0.84[EUR][1000 genomes]
rs17107650	0.84[EUR][1000 genomes]
rs17107665	0.84[EUR][1000 genomes]
rs17107672	0.84[EUR][1000 genomes]
rs17107673	0.84[EUR][1000 genomes]
rs17107676	0.84[EUR][1000 genomes]
rs17107680	0.84[EUR][1000 genomes]
rs17107705	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17599451	1.00[AFR][1000 genomes]
rs17599528	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17641707	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17718366	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17718385	0.84[EUR][1000 genomes]
rs17718403	0.84[EUR][1000 genomes]
rs17718420	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17718511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17718535	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17718737	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17774892	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17774947	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17775044	0.84[EUR][1000 genomes]
rs17775080	0.84[EUR][1000 genomes]
rs17775092	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17775104	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1833769	0.84[EUR][1000 genomes]
rs2032866	0.84[EUR][1000 genomes]
rs2052530	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2112768	0.84[EUR][1000 genomes]
rs2112769	0.84[EUR][1000 genomes]
rs2287774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2303069	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3752677	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777138	1.00[EUR][1000 genomes]
rs3815734	0.92[EUR][1000 genomes]
rs4705050	0.84[EUR][1000 genomes]
rs4705051	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4705052	0.84[EUR][1000 genomes]
rs4705053	0.84[EUR][1000 genomes]
rs4705219	0.84[EUR][1000 genomes]
rs4705220	0.84[EUR][1000 genomes]
rs5014785	0.84[EUR][1000 genomes]
rs56714312	0.81[EUR][1000 genomes]
rs56945766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57608902	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58212044	0.84[EUR][1000 genomes]
rs58237290	0.84[EUR][1000 genomes]
rs58359628	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58789871	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs58923221	0.84[EUR][1000 genomes]
rs59133736	0.84[EUR][1000 genomes]
rs59140447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59581675	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59900981	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60978485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61547850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61612041	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6872206	0.81[EUR][1000 genomes]
rs6873949	0.84[EUR][1000 genomes]
rs6881420	0.84[EUR][1000 genomes]
rs6891750	0.84[EUR][1000 genomes]
rs6892970	0.84[EUR][1000 genomes]
rs6896204	0.84[EUR][1000 genomes]
rs73269110	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73269112	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73269121	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73271110	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73794613	0.81[EUR][1000 genomes]
rs73794614	0.84[EUR][1000 genomes]
rs73794615	0.84[EUR][1000 genomes]
rs73794633	0.84[EUR][1000 genomes]
rs7703112	0.84[EUR][1000 genomes]
rs7705278	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7706528	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7714855	0.84[EUR][1000 genomes]
rs7719473	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7721002	0.84[EUR][1000 genomes]
rs7727019	0.84[EUR][1000 genomes]
rs7733255	0.84[EUR][1000 genomes]
rs953310	0.84[EUR][1000 genomes]
rs984836	0.84[EUR][1000 genomes]
rs9885178	0.81[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	nsv1033838	chr5:147360521-147484014	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv933225	chr5:147395849-147486560	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv883015	chr5:147404281-147751035	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv830515	chr5:147460852-147602247	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147450400-147469000	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr5:147450600-147468600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:147450800-147474000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr5:147451000-147470000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr5:147454000-147470000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:147455600-147469000	Weak transcription	Esophagus	oesophagus
7	chr5:147462600-147471600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:147463200-147466800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:147464000-147469800	Enhancers	Hela-S3	cervix
10	chr5:147464200-147491200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr5:147464400-147469800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr5:147464400-147488800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:147465200-147467200	Enhancers	NHEK	skin
14	chr5:147465400-147467200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:147465600-147466200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:147465600-147469000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:147466000-147466200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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