Variant report

Variant	rs4793889
Chromosome Location	chr17:46592352-46592353
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: 48 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1022088	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs1042818	0.88[EUR][1000 genomes]
rs1042822	0.88[EUR][1000 genomes]
rs11868098	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12602539	0.90[EUR][1000 genomes]
rs12603976	0.89[EUR][1000 genomes]
rs12938390	0.90[EUR][1000 genomes]
rs12939811	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12946855	0.88[EUR][1000 genomes]
rs12946931	0.90[EUR][1000 genomes]
rs12947405	0.90[EUR][1000 genomes]
rs12951076	0.87[EUR][1000 genomes]
rs17703636	0.94[EUR][1000 genomes]
rs17703660	0.94[EUR][1000 genomes]
rs2202895	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2229302	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2326012	0.90[EUR][1000 genomes]
rs34378400	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35621842	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4793854	0.86[CEU][hapmap];0.82[CHB][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4793870	0.86[ASN][1000 genomes]
rs55859232	0.91[EUR][1000 genomes]
rs56038617	0.91[EUR][1000 genomes]
rs56115209	0.86[EUR][1000 genomes]
rs56128659	0.90[EUR][1000 genomes]
rs62065846	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066689	0.93[EUR][1000 genomes]
rs62066693	0.90[EUR][1000 genomes]
rs6504281	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6504340	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs7207109	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs7207171	0.87[EUR][1000 genomes]
rs7222242	0.94[EUR][1000 genomes]
rs7225995	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8064626	0.94[EUR][1000 genomes]
rs8066613	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8071207	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8072250	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8073963	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs8074125	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs8079617	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9904760	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9905940	0.86[EUR][1000 genomes]
rs9906950	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9989493	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4793889	HOXB2	cis	uninvolved skin	skin_eQTL
rs4793889	HOXB-AS1	cis	Whole Blood	GTEx
rs4793889	HOXB2	cis	Whole Blood	GTEx
rs4793889	HOXB2	cis	Muscle Skeletal	GTEx
rs4793889	HOXB2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:19 , 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	chr17:46591000-46592400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr17:46591200-46599400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr17:46591400-46592400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr17:46591600-46592600	Enhancers	HSMM	muscle
7	chr17:46591800-46592400	Bivalent Enhancer	NH-A	brain
8	chr17:46591800-46592800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr17:46592000-46592400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr17:46592000-46592800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr17:46592000-46592800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr17:46592000-46593000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr17:46592000-46596800	Weak transcription	K562	blood
14	chr17:46592000-46604000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr17:46592200-46592400	Enhancers	Primary hematopoietic stem cells	blood
16	chr17:46592200-46592600	Enhancers	GM12878-XiMat	blood
17	chr17:46592200-46592800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr17:46592200-46593600	Weak transcription	A549	lung
19	chr17:46592200-46599400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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