Variant report

Variant	rs12602539
Chromosome Location	chr17:46617459-46617460
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:46616545-46629919	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr17:46616973-46622292	K562	blood:	n/a	n/a
3	CTCF	chr17:46617340-46617490	HEK293	kidney:	n/a	n/a
4	RCOR1	chr17:46616288-46617988	IMR90	lung:	n/a	n/a
5	POLR2A	chr17:46617272-46617847	K562	blood:	n/a	n/a
6	POLR2A	chr17:46617169-46618159	K562	blood:	n/a	n/a
7	POLR2A	chr17:46617328-46617628	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr17:46617294-46617932	K562	blood:	n/a	n/a
9	RCOR1	chr17:46617443-46618061	K562	blood:	n/a	n/a
10	POLR2A	chr17:46617177-46620098	PANC-1	pancreas:	n/a	n/a

Variant related genes	Relation type
HOXB-AS1	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1042818	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1042822	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1062037	0.80[AFR][1000 genomes]
rs11868098	0.87[EUR][1000 genomes]
rs12603976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12938390	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12939811	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12946855	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12946931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12947405	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12951076	0.87[AFR][1000 genomes];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[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2326012	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34378400	0.90[EUR][1000 genomes]
rs35621842	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4793854	0.82[EUR][1000 genomes]
rs4793889	0.90[EUR][1000 genomes]
rs55859232	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56038617	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56115209	0.96[EUR][1000 genomes]
rs56128659	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62065846	0.91[EUR][1000 genomes]
rs62066689	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62066693	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6504340	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207109	0.91[EUR][1000 genomes];0.83[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];0.86[ASN][1000 genomes]
rs8074125	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8079617	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9904760	0.87[EUR][1000 genomes]
rs9905940	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9906950	0.83[EUR][1000 genomes]
rs9989493	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
11	nsv575480	chr17:46617019-46684929	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Enhancers Weak transcription 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	322 gene(s)	inside rSNPs	diseases
12	nsv908582	chr17:46617019-46698710	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
13	nsv908583	chr17:46617019-46704536	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12602539	HOXB2	cis	Whole Blood	GTEx
rs12602539	HOXB2	cis	lung	GTEx
rs12602539	HOXB-AS1	cis	Whole Blood	GTEx
rs12602539	HOXB2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:45 , 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	chr17:46614800-46618400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr17:46615200-46618400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr17:46615400-46619600	Weak transcription	A549	lung
5	chr17:46615800-46618000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr17:46616000-46618400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr17:46616000-46618400	Enhancers	NHDF-Ad	bronchial
8	chr17:46616200-46617800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr17:46616200-46618000	Enhancers	HSMMtube	muscle
10	chr17:46616200-46618200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr17:46616200-46618400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr17:46616600-46618000	Enhancers	K562	blood
13	chr17:46616600-46618400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr17:46616600-46618400	Enhancers	NHEK	skin
15	chr17:46616800-46617600	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr17:46616800-46617800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr17:46616800-46618200	Bivalent Enhancer	Fetal Lung	lung
18	chr17:46616800-46618400	Genic enhancers	Fetal Stomach	stomach
19	chr17:46616800-46618400	Enhancers	HMEC	breast
20	chr17:46617000-46617600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr17:46617000-46617800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr17:46617000-46617800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr17:46617000-46618400	Weak transcription	Aorta	Aorta
24	chr17:46617000-46618400	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr17:46617200-46617600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr17:46617200-46617600	Flanking Active TSS	Fetal Kidney	kidney
27	chr17:46617200-46617800	Enhancers	Colon Smooth Muscle	Colon
28	chr17:46617200-46618000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr17:46617200-46618400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
30	chr17:46617200-46618400	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr17:46617400-46617600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
32	chr17:46617400-46617600	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr17:46617400-46617600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr17:46617400-46617600	Bivalent Enhancer	NH-A	brain
35	chr17:46617400-46617800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr17:46617400-46617800	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr17:46617400-46617800	Flanking Active TSS	NHLF	lung
38	chr17:46617400-46618200	Enhancers	Rectal Smooth Muscle	rectum
39	chr17:46617400-46618400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr17:46617400-46618400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
41	chr17:46617400-46618400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr17:46617400-46618400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr17:46617400-46618400	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr17:46617400-46618400	Enhancers	HSMM	muscle
45	chr17:46617400-46618600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell

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