Variant report

Variant	rs1529334
Chromosome Location	chr17:46671792-46671793
allele	C/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	TCF12	chr17:46671180-46671847	ECC-1	luminal epithelium:	n/a	n/a
2	MAZ	chr17:46669362-46676749	IMR90	lung:	n/a	chr17:46669880-46669890 chr17:46671209-46671222 chr17:46671209-46671222 chr17:46669884-46669894 chr17:46673053-46673063
3	REST	chr17:46671334-46672252	PANC-1	pancreas:	n/a	n/a
4	CTCF	chr17:46671660-46671810	HPAF	blood vessel:	n/a	n/a
5	SIN3AK20	chr17:46670500-46672191	PANC-1	pancreas:	n/a	n/a
6	SRF	chr17:46670895-46671873	ECC-1	luminal epithelium:	n/a	chr17:46671158-46671175 chr17:46671163-46671176 chr17:46671164-46671181 chr17:46671165-46671176 chr17:46671163-46671174 chr17:46671162-46671177 chr17:46671165-46671179 chr17:46671165-46671174 chr17:46671164-46671175 chr17:46671161-46671179
7	CTBP2	chr17:46671319-46673025	H1-hESC	embryonic stem cell:	n/a	n/a
8	SUZ12	chr17:46670436-46673044	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr17:46670920-46671829	A549	lung:	n/a	chr17:46671401-46671414 chr17:46671400-46671416 chr17:46671399-46671417
10	SIN3AK20	chr17:46670331-46675986	PANC-1	pancreas:	n/a	n/a
11	KAP1	chr17:46671567-46671996	U2OS	brain:	n/a	n/a
12	REST	chr17:46671298-46671888	A549	lung:	n/a	n/a
13	CHD1	chr17:46662335-46676284	IMR90	lung:	n/a	chr17:46662455-46662465 chr17:46670083-46670093 chr17:46669891-46669901
14	CTCF	chr17:46670500-46671977	SK-N-SH	brain:	n/a	chr17:46671401-46671414 chr17:46671400-46671416 chr17:46671399-46671417
15	SUZ12	chr17:46669440-46680361	NT2-D1	testis:	n/a	n/a
16	MXI1	chr17:46670335-46673027	IMR90	lung:	n/a	n/a
17	JUND	chr17:46671162-46671960	A549	lung:	n/a	chr17:46671173-46671182
18	TCF7L2	chr17:46671229-46672791	PANC-1	pancreas:	n/a	chr17:46671659-46671673 chr17:46671661-46671670
19	TCF12	chr17:46671190-46672199	A549	lung:	n/a	n/a
20	ZNF263	chr17:46671257-46671980	HEK293-T-REx	kidney:	n/a	chr17:46671346-46671367
21	POLR2A	chr17:46670404-46672018	ECC-1	luminal epithelium:	n/a	n/a
22	BCL3	chr17:46671083-46672083	A549	lung:	n/a	chr17:46671771-46671780 chr17:46671830-46671838
23	RAD21	chr17:46671002-46671828	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr17:46671117-46672132	SK-N-MC	brain:	n/a	n/a
25	POLR2A	chr17:46655911-46684927	PANC-1	pancreas:	n/a	n/a
26	FOSL2	chr17:46671218-46671959	A549	lung:	n/a	n/a
27	EP300	chr17:46670616-46671914	ECC-1	luminal epithelium:	n/a	chr17:46671847-46671863
28	CTCF	chr17:46671700-46671850	HVMF	connective:	n/a	n/a
29	POLR2A	chr17:46671287-46671833	HUVEC	blood vessel:	n/a	n/a
30	CTCF	chr17:46671700-46671850	GM12868	blood:	n/a	n/a
31	POLR2A	chr17:46671195-46673088	ECC-1	luminal epithelium:	n/a	n/a
32	TCF7L2	chr17:46671367-46671990	HEK293	kidney:	n/a	chr17:46671659-46671673 chr17:46671661-46671670
33	KAP1	chr17:46671297-46671980	HEK293	kidney:	n/a	n/a
34	POLR2A	chr17:46670513-46672579	IMR90	lung:	n/a	n/a
35	POLR2A	chr17:46645331-46684907	PANC-1	pancreas:	n/a	n/a
36	POLR2A	chr17:46670763-46672127	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46451418..46452271-chr17:46671355..46671898,2	MCF-7	breast:
2	chr17:46422046..46424668-chr17:46671390..46673476,2	K562	blood:
3	chr17:46429252..46429853-chr17:46671324..46671880,2	K562	blood:

Variant related genes	Relation type
HOXB5	TF binding region
HOXB3	TF binding region
HOXB-AS3	TF binding region
ENSG00000141293	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1062037	0.83[ASN][1000 genomes]
rs1123630	0.88[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12939811	1.00[JPT][hapmap]
rs12952262	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2229302	1.00[JPT][hapmap]
rs28575348	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3087996	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35825473	0.83[ASN][1000 genomes]
rs4646993	0.87[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4793589	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4793938	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4793939	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4793943	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4793951	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6504340	1.00[JPT][hapmap]
rs66459980	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67412921	0.83[ASN][1000 genomes]
rs7207109	1.00[JPT][hapmap]
rs8073963	1.00[JPT][hapmap]
rs8074125	1.00[JPT][hapmap]
rs8079617	1.00[JPT][hapmap]
rs872760	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9896015	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9909884	0.88[CEU][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9912500	0.87[CEU][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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
14	nsv833471	chr17:46617787-46783345	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers 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	356 gene(s)	inside rSNPs	diseases
15	nsv908584	chr17:46618926-46735520	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS 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	348 gene(s)	inside rSNPs	diseases
16	nsv457822	chr17:46620402-46698710	Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
17	nsv575481	chr17:46620402-46698710	Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh 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	334 gene(s)	inside rSNPs	diseases
18	nsv457823	chr17:46620402-46704536	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS 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	342 gene(s)	inside rSNPs	diseases
19	nsv575482	chr17:46620402-46704536	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
20	nsv457824	chr17:46625519-46693491	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised 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	332 gene(s)	inside rSNPs	diseases
21	nsv575483	chr17:46625519-46693491	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1529334	HOXB2	cis	cerebellum	SCAN
rs1529334	CNP	cis	parietal	SCAN
rs1529334	PNPO	cis	parietal	SCAN
rs1529334	HOXB2	cis	lung	GTEx
rs1529334	HOXB2	cis	Thyroid	GTEx
rs1529334	SLC35B1	cis	cerebellum	SCAN
rs1529334	HOXB2	cis	Adipose Subcutaneous	GTEx
rs1529334	HOXB2	cis	multi-tissue	Pritchard

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46663200-46672000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr17:46665600-46672400	Active TSS	NHDF-Ad	bronchial
3	chr17:46666400-46678600	Weak transcription	Hela-S3	cervix
4	chr17:46669000-46672200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr17:46669200-46672000	Active TSS	Rectal Smooth Muscle	rectum
6	chr17:46669200-46672400	Active TSS	Fetal Kidney	kidney
7	chr17:46669200-46672400	Active TSS	NHLF	lung
8	chr17:46669800-46671800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr17:46670000-46672000	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr17:46670000-46672200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr17:46671000-46671800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr17:46671000-46671800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
13	chr17:46671000-46671800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr17:46671000-46672000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
15	chr17:46671000-46672000	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr17:46671000-46672400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr17:46671000-46672600	Enhancers	HUVEC	blood vessel
18	chr17:46671000-46673400	Weak transcription	Pancreas	Pancrea
19	chr17:46671000-46676200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
20	chr17:46671200-46671800	Active TSS	Colonic Mucosa	Colon
21	chr17:46671200-46672000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr17:46671200-46673000	Genic enhancers	Rectal Mucosa Donor 31	rectum
23	chr17:46671200-46674600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr17:46671400-46671800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr17:46671400-46671800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
26	chr17:46671400-46671800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
27	chr17:46671400-46671800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
28	chr17:46671400-46671800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr17:46671400-46671800	Flanking Active TSS	A549	lung
30	chr17:46671400-46671800	Bivalent Enhancer	GM12878-XiMat	blood
31	chr17:46671400-46671800	Enhancers	HSMM	muscle
32	chr17:46671400-46671800	Bivalent Enhancer	NHEK	skin
33	chr17:46671400-46672000	Flanking Bivalent TSS/Enh	Fetal Lung	lung
34	chr17:46671400-46672000	Bivalent/Poised TSS	HepG2	liver
35	chr17:46671400-46672000	Enhancers	HSMMtube	muscle
36	chr17:46671400-46673600	Weak transcription	Right Atrium	heart
37	chr17:46671400-46674200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr17:46671400-46674600	Bivalent Enhancer	Fetal Muscle Leg	muscle
39	chr17:46671600-46671800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
40	chr17:46671600-46671800	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr17:46671600-46671800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
42	chr17:46671600-46671800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
43	chr17:46671600-46671800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr17:46671600-46671800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr17:46671600-46671800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
46	chr17:46671600-46671800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
47	chr17:46671600-46671800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr17:46671600-46671800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr17:46671600-46671800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr17:46671600-46671800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum

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