Variant report

Variant	rs12947405
Chromosome Location	chr17:46614755-46614756
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1042818	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1042822	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11868098	0.87[EUR][1000 genomes]
rs12602539	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12603976	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12938390	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12939811	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12946855	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12946931	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12951076	0.97[EUR][1000 genomes]
rs17703636	0.86[EUR][1000 genomes]
rs17703660	0.86[EUR][1000 genomes]
rs2202895	0.83[EUR][1000 genomes]
rs2229302	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2326012	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34378400	0.90[EUR][1000 genomes]
rs35621842	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4793854	0.82[EUR][1000 genomes]
rs4793889	0.90[EUR][1000 genomes]
rs55859232	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56038617	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56115209	0.96[EUR][1000 genomes]
rs56128659	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62065846	0.91[EUR][1000 genomes]
rs62066689	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62066693	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6504340	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7207109	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7207171	0.81[EUR][1000 genomes]
rs7222242	0.86[EUR][1000 genomes]
rs7225995	0.91[EUR][1000 genomes]
rs8064626	0.86[EUR][1000 genomes]
rs8066613	0.90[EUR][1000 genomes]
rs8071207	0.84[EUR][1000 genomes]
rs8072250	0.85[EUR][1000 genomes]
rs8073963	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8074125	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8079617	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9904760	0.87[EUR][1000 genomes]
rs9905940	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9906950	0.83[EUR][1000 genomes]
rs9989493	0.91[EUR][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	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
9	nsv908580	chr17:46609103-46698710	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	335 gene(s)	inside rSNPs	diseases
10	nsv908581	chr17:46610646-46735520	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription 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	349 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12947405	HOXB-AS1	cis	Whole Blood	GTEx
rs12947405	HOXB2	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46610200-46618400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr17:46611400-46615200	Enhancers	K562	blood
3	chr17:46612200-46616400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr17:46613000-46615200	Enhancers	Muscle Satellite Cultured Cells	--
5	chr17:46613000-46615200	Enhancers	NHLF	lung
6	chr17:46613200-46615800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr17:46613800-46614800	Weak transcription	Fetal Stomach	stomach
8	chr17:46613800-46615000	Enhancers	HSMM	muscle
9	chr17:46613800-46615400	Enhancers	A549	lung
10	chr17:46613800-46615600	Enhancers	NHDF-Ad	bronchial
11	chr17:46614000-46615000	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr17:46614000-46615000	Enhancers	Hela-S3	cervix
13	chr17:46614000-46615000	Enhancers	HSMMtube	muscle
14	chr17:46614200-46616200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr17:46614400-46614800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr17:46614400-46614800	Weak transcription	NH-A	brain
17	chr17:46614600-46614800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr17:46614600-46615000	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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