Variant report

Variant	rs2462963
Chromosome Location	chr17:38861757-38861758
allele	A/C
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	POLR2A	chr17:38861542-38861799	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr17:38861567-38861884	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr17:38861472-38861908	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38802997..38805414-chr17:38859614..38861857,2	MCF-7	breast:

Variant related genes	Relation type
KRT24	TF binding region
ENSG00000073584	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1029792	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1048572	0.82[EUR][1000 genomes]
rs1048573	0.82[EUR][1000 genomes]
rs12943859	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2008469	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2014704	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2109223	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2159430	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2253717	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2315020	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2429549	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2462962	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2462964	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2462970	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2469818	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3752026	0.81[EUR][1000 genomes]
rs4890119	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4890122	0.84[ASN][1000 genomes]
rs58630924	0.86[ASN][1000 genomes]
rs6503547	0.81[EUR][1000 genomes]
rs6503549	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7209467	0.82[ASN][1000 genomes]
rs7209735	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7212255	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7219483	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7223332	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7223354	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs726848	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs758630	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8068721	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8076587	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs917593	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs917595	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9896791	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9906785	0.82[EUR][1000 genomes]
rs9915135	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431626	chr17:38770965-38999722	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv908225	chr17:38776406-38868480	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2462963	KRT24	cis	Esophagus Mucosa	GTEx
rs2462963	CCR7	Cis_1M	lymphoblastoid	RTeQTL
rs2462963	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL
rs2462963	KRT222	cis	Nerve Tibial	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38853400-38864000	Weak transcription	A549	lung
2	chr17:38853800-38864000	Weak transcription	Right Atrium	heart
3	chr17:38854000-38861800	Weak transcription	HMEC	breast
4	chr17:38854000-38875800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr17:38856800-38863600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr17:38859800-38862400	Enhancers	NHEK	skin
7	chr17:38860000-38861800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr17:38860000-38864000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr17:38860000-38864600	Weak transcription	Placenta	Placenta
10	chr17:38860000-38890200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr17:38860600-38862600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr17:38861600-38862000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr17:38861600-38864200	Enhancers	Hela-S3	cervix

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