Variant report

Variant	rs458304
Chromosome Location	chr5:102874719-102874720
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	chr5:102873676..102876044-chr5:102879695..102881273,2	MCF-7	breast:
2	chr5:102873569..102875593-chr5:102896937..102898488,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10044216	0.95[ASN][1000 genomes]
rs10045774	0.94[ASN][1000 genomes]
rs10057908	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11750125	0.93[ASN][1000 genomes]
rs11956617	0.85[ASN][1000 genomes]
rs159164	0.83[ASN][1000 genomes]
rs159165	0.83[ASN][1000 genomes]
rs159166	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs159167	0.81[ASN][1000 genomes]
rs159168	0.81[ASN][1000 genomes]
rs159169	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs169799	0.95[ASN][1000 genomes]
rs169800	0.95[ASN][1000 genomes]
rs1813569	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1988929	0.95[ASN][1000 genomes]
rs2048150	0.95[ASN][1000 genomes]
rs2112340	0.90[ASN][1000 genomes]
rs2401010	0.92[ASN][1000 genomes]
rs251162	0.83[ASN][1000 genomes]
rs251163	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs294041	0.97[ASN][1000 genomes]
rs294044	0.98[ASN][1000 genomes]
rs294045	0.95[ASN][1000 genomes]
rs294048	0.95[ASN][1000 genomes]
rs294098	1.00[ASN][1000 genomes]
rs3734087	0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs409474	0.90[ASN][1000 genomes]
rs443022	0.92[ASN][1000 genomes]
rs4703253	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4703254	0.94[ASN][1000 genomes]
rs6596534	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7724372	0.95[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs822416	0.95[ASN][1000 genomes]
rs822418	0.95[ASN][1000 genomes]
rs9327886	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882523	chr5:102687151-103342745	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1031600	chr5:102728430-103013575	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1025561	chr5:102744280-103152495	Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv537832	chr5:102744280-103152495	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1025859	chr5:102744479-103710290	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv537833	chr5:102744479-103710290	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs458304	PPIP5K2	cis	cerebellum	SCAN
rs458304	PPIP5K2	cis	Whole Blood	GTEx
rs458304	NUDT12	Cis_1M	lymphoblastoid	RTeQTL
rs458304	NUDT12	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:102874200-102897400	Weak transcription	Pancreas	Pancrea

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