Variant report

Variant	rs9563063
Chromosome Location	chr13:52125748-52125749
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	SIN3AK20	chr13:52125651-52125888	PFSK-1	brain:	n/a	n/a
2	FOXA1	chr13:52125624-52125946	HepG2	liver:	n/a	n/a
3	SIN3AK20	chr13:52125637-52125869	PFSK-1	brain:	n/a	n/a
4	FOXA1	chr13:52125622-52125993	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:52097331..52099871-chr13:52124586..52126544,2	MCF-7	breast:
2	chr13:52026832..52028649-chr13:52125525..52127655,3	MCF-7	breast:
3	chr13:52124143..52125807-chr13:52127264..52129826,2	K562	blood:

Variant related genes	Relation type
MIR4703	TF binding region
ENSG00000102786	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000224892	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1024271	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12585249	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17075902	0.85[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap]
rs17532412	1.00[YRI][hapmap]
rs3803201	0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap]
rs3825410	0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap]
rs4075628	0.95[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4625625	0.85[CHB][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs4941703	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4943005	1.00[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4943009	0.85[GIH][hapmap]
rs745374	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9316547	0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs9316548	0.93[ASN][1000 genomes]
rs9316551	0.81[CHB][hapmap]
rs9535744	1.00[YRI][hapmap]
rs9563061	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs9563065	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9563066	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9563067	0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap]
rs9568621	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs9568633	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9568644	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9568650	0.85[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap]
rs9805172	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

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	esv1797261	chr13:52100949-52139113	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52116800-52132000	Weak transcription	Pancreas	Pancrea
2	chr13:52117000-52126200	Weak transcription	Adipose Nuclei	Adipose
3	chr13:52122800-52126800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr13:52123600-52125800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr13:52123800-52126200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr13:52123800-52129200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr13:52123800-52129400	Weak transcription	NHEK	skin
8	chr13:52124000-52125800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr13:52124000-52126000	Weak transcription	K562	blood
10	chr13:52124000-52129400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr13:52124000-52130200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr13:52124200-52131600	Weak transcription	HepG2	liver
13	chr13:52124400-52132000	Weak transcription	A549	lung
14	chr13:52124800-52126000	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr13:52125200-52126600	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr13:52125400-52125800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr13:52125600-52126000	Enhancers	Primary hematopoietic stem cells	blood
18	chr13:52125600-52127000	Enhancers	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links