Variant report

Variant	rs62066689
Chromosome Location	chr17:46609092-46609093
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	chr17:46598935..46600877-chr17:46608428..46610318,2	MCF-7	breast:
2	chr17:46601060..46603214-chr17:46608437..46610558,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1042818	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1042822	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11868098	0.90[EUR][1000 genomes]
rs12602539	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12603976	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12938390	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12939811	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12946855	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12946931	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12947405	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12951076	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs17703636	0.89[EUR][1000 genomes]
rs17703660	0.89[EUR][1000 genomes]
rs2202895	0.86[EUR][1000 genomes]
rs2229302	0.93[AFR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2326012	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34378400	0.94[EUR][1000 genomes]
rs35621842	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4793854	0.85[EUR][1000 genomes]
rs4793889	0.93[EUR][1000 genomes]
rs55859232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56038617	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56115209	0.93[EUR][1000 genomes]
rs56128659	0.93[AFR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62065846	0.94[EUR][1000 genomes]
rs62066693	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6504281	0.82[EUR][1000 genomes]
rs6504340	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7207109	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7207171	0.83[EUR][1000 genomes]
rs7222242	0.89[EUR][1000 genomes]
rs7225995	0.94[EUR][1000 genomes]
rs8064626	0.89[EUR][1000 genomes]
rs8066613	0.94[EUR][1000 genomes]
rs8071207	0.87[EUR][1000 genomes]
rs8072250	0.88[EUR][1000 genomes]
rs8073963	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8074125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8079617	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9904760	0.90[EUR][1000 genomes]
rs9905940	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9906950	0.86[EUR][1000 genomes]
rs9989493	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
6	nsv532113	chr17:46598247-47588570	Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	453 gene(s)	inside rSNPs	diseases
7	esv2758459	chr17:46602673-46836837	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised 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	364 gene(s)	inside rSNPs	diseases
8	esv2758694	chr17:46602673-46836837	Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs62066689	HOXB2	cis	Whole Blood	GTEx
rs62066689	HOXB-AS1	cis	Whole Blood	GTEx
rs62066689	HOXB2	cis	Adipose Subcutaneous	GTEx
rs62066689	HOXB2	cis	lung	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46603600-46609200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
2	chr17:46605000-46610000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
3	chr17:46605200-46613000	Weak transcription	NHLF	lung
4	chr17:46605800-46609800	Weak transcription	Right Atrium	heart
5	chr17:46606200-46609200	Weak transcription	A549	lung
6	chr17:46606600-46609800	Weak transcription	K562	blood
7	chr17:46606600-46610600	Weak transcription	HSMMtube	muscle
8	chr17:46608400-46609200	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
9	chr17:46608400-46609400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr17:46608800-46609200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
11	chr17:46608800-46609200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
12	chr17:46608800-46609800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
13	chr17:46608800-46611000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
14	chr17:46609000-46609600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
15	chr17:46609000-46609800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr17:46609000-46609800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
17	chr17:46609000-46610400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr17:46609000-46611400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell

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