Variant report

Variant	rs9646103
Chromosome Location	chr13:39474658-39474659
allele	A/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	chr13:39474322-39474740	H1-hESC	embryonic stem cell:	n/a	chr13:39474540-39474559
2	CTCF	chr13:39474520-39474670	SAEC	small airway:	n/a	chr13:39474537-39474558 chr13:39474548-39474557
3	CTCF	chr13:39474520-39474670	HPF	lung:	n/a	chr13:39474537-39474558 chr13:39474548-39474557
4	CTCF	chr13:39474441-39474665	MCF-7	breast:	n/a	chr13:39474537-39474558 chr13:39474548-39474557
5	CTCF	chr13:39474560-39474710	GM12874	blood:	n/a	n/a
6	CTCF	chr13:39474520-39474670	HFF-Myc	foreskin:	n/a	chr13:39474537-39474558 chr13:39474548-39474557
7	CTCF	chr13:39474520-39474670	GM12865	blood:	n/a	chr13:39474537-39474558 chr13:39474548-39474557
8	CTCF	chr13:39474338-39474768	MCF-7	breast:	n/a	chr13:39474537-39474558 chr13:39474548-39474557
9	CTCF	chr13:39474520-39474670	Caco-2	colon:	n/a	chr13:39474537-39474558 chr13:39474548-39474557
10	CTCF	chr13:39474540-39474690	HFF-Myc	foreskin:	n/a	chr13:39474548-39474557
11	CTCF	chr13:39474520-39474670	RPTEC	kidney:	n/a	chr13:39474537-39474558 chr13:39474548-39474557
12	CTCF	chr13:39474369-39474669	K562	blood:	n/a	chr13:39474537-39474558 chr13:39474548-39474557
13	CTCF	chr13:39474560-39474710	HepG2	liver:	n/a	n/a
14	CTCF	chr13:39474336-39474724	H1-hESC	embryonic stem cell:	n/a	chr13:39474537-39474558 chr13:39474548-39474557
15	CTCF	chr13:39474383-39474712	GM12878	blood:	n/a	chr13:39474537-39474558 chr13:39474548-39474557
16	CTCF	chr13:39474620-39474770	A549	lung:	n/a	n/a
17	CTCF	chr13:39474520-39474670	AG04450	lung:	n/a	chr13:39474537-39474558 chr13:39474548-39474557
18	CTCF	chr13:39474434-39474676	Medullo	brain:	n/a	chr13:39474537-39474558 chr13:39474548-39474557
19	ZNF143	chr13:39474333-39474704	H1-hESC	embryonic stem cell:	n/a	n/a
20	RAD21	chr13:39474378-39474714	H1-hESC	embryonic stem cell:	n/a	chr13:39474540-39474559
21	CTCF	chr13:39474520-39474670	HCT-116	colon:	n/a	chr13:39474537-39474558 chr13:39474548-39474557
22	SMC3	chr13:39474497-39474666	GM12878	blood:	n/a	n/a
23	CTCF	chr13:39474600-39474750	HCM	heart:	n/a	n/a
24	CTCF	chr13:39474540-39474690	HVMF	connective:	n/a	chr13:39474548-39474557
25	RAD21	chr13:39474292-39474660	H1-hESC	embryonic stem cell:	n/a	chr13:39474540-39474559
26	CTCF	chr13:39474520-39474670	Hela-S3	cervix:	n/a	chr13:39474537-39474558 chr13:39474548-39474557
27	CTCF	chr13:39474520-39474670	K562	blood:	n/a	chr13:39474537-39474558 chr13:39474548-39474557

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:39440389..39441031-chr13:39474107..39474895,2	MCF-7	breast:

Variant related genes	Relation type
PLA2G12AP2	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10870726	0.81[EUR][1000 genomes]
rs1894102	0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2156810	0.80[ASN][1000 genomes]
rs36098057	0.84[EUR][1000 genomes]
rs4492928	0.80[EUR][1000 genomes]
rs9315626	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9532300	0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9532301	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9532302	0.84[EUR][1000 genomes]
rs9532303	0.84[EUR][1000 genomes]
rs9548534	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9548537	0.82[ASN][1000 genomes]
rs9548541	0.81[CEU][hapmap];0.91[CHB][hapmap];0.83[EUR][1000 genomes]
rs9548543	0.81[EUR][1000 genomes]
rs9548547	0.81[CEU][hapmap]
rs9566378	0.80[EUR][1000 genomes]
rs9576641	0.84[EUR][1000 genomes]
rs9576642	0.84[EUR][1000 genomes]
rs9646104	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39463000-39476200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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