Variant report

Variant	rs4793937
Chromosome Location	chr17:46663850-46663851
allele	A/G
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	MAZ	chr17:46662285-46664134	IMR90	lung:	n/a	n/a
2	MTA3	chr17:46662378-46664216	GM12878	blood:	n/a	n/a
3	RUNX3	chr17:46663642-46663969	GM12878	blood:	n/a	n/a
4	EP300	chr17:46663845-46664103	GM12878	blood:	n/a	chr17:46663847-46663863 chr17:46663880-46663896
5	CTCF	chr17:46663828-46663912	GM19238	blood:	n/a	n/a
6	CTCF	chr17:46663760-46663910	HMF	breast:	n/a	n/a
7	POLR2A	chr17:46663610-46663991	HCT-116	colon:	n/a	n/a
8	RAD21	chr17:46662302-46663990	HCT-116	colon:	n/a	chr17:46663448-46663458 chr17:46663122-46663136 chr17:46663448-46663460
9	POU2F2	chr17:46663661-46663997	GM12891	blood:	n/a	n/a
10	CTBP2	chr17:46662351-46663925	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr17:46663567-46663867	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr17:46662730-46664028	HUVEC	blood vessel:	n/a	n/a
13	ZNF263	chr17:46662541-46663982	HEK293-T-REx	kidney:	n/a	chr17:46663483-46663492
14	CHD1	chr17:46662335-46676284	IMR90	lung:	n/a	chr17:46662455-46662465 chr17:46670083-46670093 chr17:46669891-46669901
15	RUNX3	chr17:46663565-46664054	GM12878	blood:	n/a	n/a
16	SUZ12	chr17:46662649-46665098	NT2-D1	testis:	n/a	n/a
17	RCOR1	chr17:46663680-46663878	GM12878	blood:	n/a	n/a
18	EGR1	chr17:46663671-46663917	GM12878	blood:	n/a	chr17:46663799-46663813 chr17:46663775-46663788 chr17:46663778-46663792
19	TBL1XR1	chr17:46663795-46663916	GM12878	blood:	n/a	n/a
20	CTCF	chr17:46663779-46663907	GM19239	blood:	n/a	n/a
21	FOSL2	chr17:46662359-46663909	A549	lung:	n/a	n/a
22	RELA	chr17:46662733-46663936	GM19099	blood:	n/a	n/a
23	MAX	chr17:46663736-46663914	GM12878	blood:	n/a	n/a
24	SIN3AK20	chr17:46662148-46664308	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr17:46663671-46663960	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr17:46663617-46663979	HCT-116	colon:	n/a	n/a
27	SUZ12	chr17:46662105-46664500	H1-hESC	embryonic stem cell:	n/a	n/a
28	HMGN3	chr17:46663699-46663922	K562	blood:	n/a	n/a
29	CTCF	chr17:46663799-46663889	GM12892	blood:	n/a	n/a
30	POLR2A	chr17:46655911-46684927	PANC-1	pancreas:	n/a	n/a
31	POU2F2	chr17:46663642-46664055	GM12878	blood:	n/a	n/a
32	EGR1	chr17:46663701-46663898	K562	blood:	n/a	chr17:46663799-46663813 chr17:46663775-46663788 chr17:46663778-46663792
33	POLR2A	chr17:46663725-46663954	HUVEC	blood vessel:	n/a	n/a
34	EGR1	chr17:46663681-46663901	GM12878	blood:	n/a	chr17:46663799-46663813 chr17:46663775-46663788 chr17:46663778-46663792
35	CCNT2	chr17:46663763-46664002	K562	blood:	n/a	chr17:46663780-46663789
36	BHLHE40	chr17:46663750-46663860	GM12878	blood:	n/a	n/a
37	EP300	chr17:46662697-46663974	GM12878	blood:	n/a	chr17:46663847-46663863 chr17:46663183-46663199 chr17:46663880-46663896 chr17:46663074-46663088 chr17:46663824-46663833
38	POLR2A	chr17:46663608-46663938	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr17:46645331-46684907	PANC-1	pancreas:	n/a	n/a
40	MAZ	chr17:46663477-46664082	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46589537..46591935-chr17:46661739..46663956,2	MCF-7	breast:
2	chr17:46639764..46641981-chr17:46663009..46664957,2	MCF-7	breast:
3	chr17:46572626..46574764-chr17:46662731..46664611,2	MCF-7	breast:
4	chr17:46530850..46533321-chr17:46662351..46664282,2	K562	blood:
5	chr17:46663028..46666157-chr17:46668975..46671535,3	MCF-7	breast:

Variant related genes	Relation type
HOXB-AS3	TF binding region
MIR10A	TF binding region
HOXB3	TF binding region
ENSG00000120075	Chromatin interaction
ENSG00000233101	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1062037	0.81[ASN][1000 genomes]
rs34490194	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34822124	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35624684	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35825473	0.81[ASN][1000 genomes]
rs67412921	0.81[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4793937	HOXB2	cis	Thyroid	GTEx
rs4793937	HOXB2	cis	Whole Blood	GTEx
rs4793937	HOXB-AS1	cis	Whole Blood	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46658800-46665800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr17:46661600-46667000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr17:46661800-46664000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr17:46662000-46664600	Active TSS	NHDF-Ad	bronchial
5	chr17:46662000-46665200	Active TSS	Colon Smooth Muscle	Colon
6	chr17:46662200-46664000	Active TSS	Fetal Kidney	kidney
7	chr17:46662200-46664000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
8	chr17:46662200-46664000	Active TSS	Right Atrium	heart
9	chr17:46662200-46664200	Active TSS	Rectal Smooth Muscle	rectum
10	chr17:46662400-46664000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
11	chr17:46662400-46664000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
12	chr17:46662400-46664000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr17:46662400-46664000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr17:46662400-46664000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
15	chr17:46662400-46664000	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr17:46662400-46664200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
17	chr17:46662400-46664200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
18	chr17:46662400-46664200	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
19	chr17:46662400-46664200	Flanking Active TSS	HUVEC	blood vessel
20	chr17:46662400-46665000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr17:46662400-46665000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
22	chr17:46662400-46665600	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr17:46662400-46668000	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr17:46662600-46664000	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
25	chr17:46662600-46664000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
26	chr17:46662800-46664000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr17:46662800-46664000	Active TSS	Right Ventricle	heart
28	chr17:46663000-46664000	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
29	chr17:46663000-46664000	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
30	chr17:46663200-46664000	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood
31	chr17:46663200-46664000	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr17:46663200-46664000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
33	chr17:46663200-46664000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr17:46663200-46664000	Flanking Bivalent TSS/Enh	Placenta	Placenta
35	chr17:46663200-46664000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr17:46663200-46664200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
37	chr17:46663200-46664800	Transcr. at gene 5' and 3'	NHLF	lung
38	chr17:46663200-46665400	Flanking Active TSS	Colonic Mucosa	Colon
39	chr17:46663200-46672000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr17:46663400-46664000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr17:46663400-46664000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr17:46663400-46664000	Bivalent Enhancer	Fetal Heart	heart
43	chr17:46663400-46664000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
44	chr17:46663400-46664000	Bivalent Enhancer	Fetal Thymus	thymus
45	chr17:46663400-46664000	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr17:46663400-46664200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr17:46663400-46664400	Enhancers	Gastric	stomach
48	chr17:46663400-46666400	Enhancers	Lung	lung
49	chr17:46663600-46664000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr17:46663600-46664000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell

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