Variant report

Variant	rs12450225
Chromosome Location	chr17:46592413-46592414
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46582101..46583693-chr17:46591339..46593282,2	MCF-7	breast:
2	chr17:46585053..46590191-chr17:46590759..46593936,5	MCF-7	breast:
3	chr17:46590407..46593001-chr17:46595445..46597263,2	MCF-7	breast:
4	chr17:46590857..46593060-chr17:46597939..46599663,2	K562	blood:
5	chr17:46439319..46441570-chr17:46591385..46593925,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10514953	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10853099	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10853100	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11079824	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11079825	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11079826	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11079828	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs11651168	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11652125	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11867735	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11869101	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12603662	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1509638	0.96[AMR][1000 genomes]
rs1553748	0.81[JPT][hapmap]
rs1553754	0.85[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs1553755	0.81[JPT][hapmap]
rs1812501	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1987164	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2036764	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2325948	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2326013	0.80[EUR][1000 genomes]
rs4793564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59961340	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60154639	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60859312	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62065845	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62065847	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066684	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6504280	0.81[JPT][hapmap]
rs7214534	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72829818	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72829824	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7501529	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8077407	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs925284	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833469	chr17:46491849-46709406	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
2	esv3420538	chr17:46504944-46861553	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	369 gene(s)	inside rSNPs	diseases
3	nsv908577	chr17:46584900-46704536	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	343 gene(s)	inside rSNPs	diseases
4	nsv908578	chr17:46592413-46698710	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	335 gene(s)	inside rSNPs	diseases
5	nsv908579	chr17:46592413-46727289	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12450225	LOC100130581	cis	parietal	SCAN
rs12450225	HOXB-AS1	cis	Whole Blood	GTEx
rs12450225	SP6	cis	parietal	SCAN
rs12450225	HOXB2	Cis_1M	lymphoblastoid	RTeQTL
rs12450225	C17orf46	cis	parietal	SCAN
rs12450225	HOXB2	cis	Whole Blood	GTEx
rs12450225	KIF18B	cis	cerebellum	SCAN
rs12450225	PTRF	cis	parietal	SCAN
rs12450225	PRAC	cis	parietal	SCAN
rs12450225	HOXB3	cis	Whole Blood	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46589200-46593600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr17:46590800-46599600	Weak transcription	Right Atrium	heart
3	chr17:46591200-46599400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr17:46591600-46592600	Enhancers	HSMM	muscle
5	chr17:46591800-46592800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr17:46592000-46592800	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr17:46592000-46592800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr17:46592000-46593000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr17:46592000-46596800	Weak transcription	K562	blood
10	chr17:46592000-46604000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr17:46592200-46592600	Enhancers	GM12878-XiMat	blood
12	chr17:46592200-46592800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr17:46592200-46593600	Weak transcription	A549	lung
14	chr17:46592200-46599400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr17:46592400-46592600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
16	chr17:46592400-46592600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr17:46592400-46592600	Bivalent Enhancer	Osteobl	bone
18	chr17:46592400-46592800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
19	chr17:46592400-46592800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
20	chr17:46592400-46594800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr17:46592400-46599400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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