Variant report

Variant	rs2717048
Chromosome Location	chr2:58025937-58025938
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:58025264..58027443-chr2:58030430..58032051,2	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10204616	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1040224	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs1040225	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs10496078	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10496079	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10865304	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1106302	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11898858	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12713358	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12713370	0.89[CEU][hapmap]
rs12990792	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12997222	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1356544	0.83[EUR][1000 genomes]
rs1356545	0.83[EUR][1000 genomes]
rs1401100	0.93[GIH][hapmap];0.93[TSI][hapmap]
rs1402398	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1518395	0.89[CEU][hapmap];0.93[GIH][hapmap]
rs1568253	0.95[GIH][hapmap];0.93[TSI][hapmap]
rs1568450	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1589407	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2090793	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2204019	0.84[ASN][1000 genomes]
rs2312141	0.80[EUR][1000 genomes]
rs2312147	0.85[CEU][hapmap];0.91[GIH][hapmap]
rs2465804	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2678880	0.82[CEU][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap]
rs2678881	0.83[EUR][1000 genomes]
rs2678889	0.93[GIH][hapmap];0.93[TSI][hapmap]
rs2678897	0.88[GIH][hapmap];0.93[TSI][hapmap]
rs2678901	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2678903	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2678904	0.82[EUR][1000 genomes]
rs2678905	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2678906	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2678908	0.82[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs2678915	0.83[EUR][1000 genomes]
rs2683614	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683616	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2683619	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2683620	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2683622	0.84[ASN][1000 genomes]
rs2683625	0.87[ASN][1000 genomes]
rs2683628	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2683629	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2683634	0.83[EUR][1000 genomes]
rs2716998	0.83[ASN][1000 genomes]
rs2716999	0.84[ASN][1000 genomes]
rs2717001	0.82[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2717002	0.82[CEU][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs2717004	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2717006	0.89[CEU][hapmap]
rs2717007	0.83[EUR][1000 genomes]
rs2717015	0.80[EUR][1000 genomes]
rs2717018	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2717023	0.98[GIH][hapmap];0.92[TSI][hapmap]
rs2717024	0.98[GIH][hapmap];0.92[TSI][hapmap]
rs2717031	0.95[GIH][hapmap];0.93[TSI][hapmap]
rs2717036	0.95[GIH][hapmap];0.92[TSI][hapmap]
rs2717040	0.93[GIH][hapmap];0.93[TSI][hapmap]
rs2717056	0.83[EUR][1000 genomes]
rs2717063	0.81[EUR][1000 genomes]
rs2717068	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2717075	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2947350	0.83[ASN][1000 genomes]
rs2947351	0.84[ASN][1000 genomes]
rs2953437	0.84[ASN][1000 genomes]
rs2953438	0.84[ASN][1000 genomes]
rs2953439	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2953441	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2953443	0.87[ASN][1000 genomes]
rs3886275	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4296411	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4672223	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6545663	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6545664	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6545665	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6545677	0.85[CEU][hapmap]
rs66490669	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6730037	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6732310	0.89[CEU][hapmap];0.93[GIH][hapmap]
rs6737913	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6756221	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6761347	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7561842	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7588492	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7598169	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007118	chr2:57562051-58147588	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv874193	chr2:57758608-58066673	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1006688	chr2:57822953-58030203	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv874196	chr2:57946148-58220320	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv874197	chr2:57978858-58068741	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv834148	chr2:57979661-58119213	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv874198	chr2:57987593-58068741	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv458030	chr2:58012833-58062220	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv582095	chr2:58012833-58062220	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1010981	chr2:58013389-58205699	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2717048	VRK2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58022000-58026600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:58025400-58026200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
3	chr2:58025400-58026400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
4	chr2:58025800-58026200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:58025800-58026200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:58025800-58026600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell

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