Variant report

Variant	rs4793943
Chromosome Location	chr17:46666937-46666938
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr17:46666419-46668321	PANC-1	pancreas:	n/a	n/a
2	GATA3	chr17:46666850-46667052	MCF-7	breast:	n/a	chr17:46666917-46666926
3	GATA2	chr17:46666854-46667127	SH-SY5Y	brain:	n/a	chr17:46666917-46666926
4	CHD1	chr17:46662335-46676284	IMR90	lung:	n/a	chr17:46662455-46662465 chr17:46670083-46670093 chr17:46669891-46669901
5	GATA3	chr17:46666702-46667194	MCF-7	breast:	n/a	chr17:46666917-46666926
6	ZNF263	chr17:46664705-46668149	HEK293-T-REx	kidney:	n/a	chr17:46667558-46667579 chr17:46667189-46667198
7	POLR2A	chr17:46666701-46667235	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr17:46666889-46666937	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr17:46655911-46684927	PANC-1	pancreas:	n/a	n/a
10	SIN3AK20	chr17:46666576-46668137	PANC-1	pancreas:	n/a	n/a
11	SUZ12	chr17:46666699-46668009	H1-hESC	embryonic stem cell:	n/a	n/a
12	TCF7L2	chr17:46666676-46668209	PANC-1	pancreas:	n/a	chr17:46668157-46668164
13	POLR2A	chr17:46666936-46667264	HCT-116	colon:	n/a	n/a
14	POLR2A	chr17:46645331-46684907	PANC-1	pancreas:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:46666926-46666976	BE2_C	brain:	n/a
2	chr17:46666926-46666976	Hepatocyte	liver:	n/a
3	chr17:46666926-46666976	HepG2	liver:	n/a
4	chr17:46666926-46666976	K562	blood:	n/a
5	chr17:46666926-46666976	NHDF-neo	bronchial:	n/a
6	chr17:46666926-46666976	HCPEpiC	choroid plexus:	n/a
7	chr17:46666926-46666976	U87	brain:	n/a
8	chr17:46666926-46666976	HPAEpiC	pulmonary alveolar:	n/a
9	chr17:46666926-46666976	ECC-1	luminal epithelium:	n/a
10	chr17:46666926-46666976	IMR90	lung:	fetal
11	chr17:46666926-46666976	HMEC	breast:	n/a
12	chr17:46666926-46666976	Hela-S3	cervix:	n/a
13	chr17:46666926-46666976	SK-N-SH_RA	brain:	n/a
14	chr17:46666926-46666976	RPTEC	kidney:	n/a
15	chr17:46666926-46666976	HRPEpiC	eye:	n/a
16	chr17:46666926-46666976	GM12892	blood:	n/a
17	chr17:46666926-46666976	SKMC	muscle:	n/a
18	chr17:46666926-46666976	SAEC	small airway:	n/a
19	chr17:46666926-46666976	T-47D	breast:	n/a
20	chr17:46666926-46666976	AG09309	skin:	n/a
21	chr17:46666926-46666976	PFSK-1	brain:	n/a
22	chr17:46666926-46666976	A549	lung:	n/a
23	chr17:46666926-46666976	NHBE	bronchial:	n/a
24	chr17:46666926-46666976	AG10803	skin:	n/a
25	chr17:46666926-46666976	BJ	skin:	n/a
26	chr17:46666926-46666976	SK-N-MC	brain:	n/a
27	chr17:46666926-46666976	HCF	heart:	n/a
28	chr17:46666926-46666976	HL-60	blood:	n/a
29	chr17:46666926-46666976	SK-N-SH	brain:	n/a
30	chr17:46666926-46666976	AoSMC	blood vessel:	n/a
31	chr17:46666926-46666976	HNPCEpiC	eye:	n/a
32	chr17:46666926-46666976	NH-A	brain:	n/a
33	chr17:46666926-46666976	CMK	blood:	n/a
34	chr17:46666926-46666976	Caco-2	colon:	n/a
35	chr17:46666926-46666976	NT2-D1	testis:	n/a
36	chr17:46666926-46666976	MCF10A-Er-Src	breast:	n/a
37	chr17:46666926-46666976	HRCEpiC	kidney:	n/a
38	chr17:46666926-46666976	AG04450	lung:	fetal
39	chr17:46666926-46666976	ovcar-3	ovarian:	n/a
40	chr17:46666926-46666976	PrEC	prostate:	n/a
41	chr17:46666926-46666976	GM19239	blood:	n/a
42	chr17:46666926-46666976	MCF-7	breast:	n/a
43	chr17:46666926-46666976	HCM	heart:	n/a
44	chr17:46666926-46666976	LNCaP	prostate:	n/a
45	chr17:46666926-46666976	GM12891	blood:	n/a
46	chr17:46666926-46666976	GM12878	blood:	n/a
47	chr17:46666926-46666976	GM06990	blood:	n/a
48	chr17:46666926-46666976	HRE	kidney:	n/a
49	chr17:46666926-46666976	PANC-1	pancreas:	n/a
50	chr17:46666926-46666976	HAEpiC	amniotic membrane:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:46664818..46667926-chr17:46672135..46673972,3	MCF-7	breast:

No data

Variant related genes	Relation type
HOXB-AS3	TF binding region
HOXB-AS3	CpG island
ENSG00000233101	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1062037	0.90[ASN][1000 genomes]
rs1123630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12939324	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12939811	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs12952262	0.87[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1529334	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]
rs2229302	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs3087996	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34490194	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34527992	0.80[EUR][1000 genomes]
rs34822124	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35621842	0.80[CEU][hapmap]
rs35624684	0.83[EUR][1000 genomes]
rs35825473	0.90[ASN][1000 genomes]
rs4239158	0.87[CEU][hapmap]
rs4646993	0.87[CEU][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4793589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4793938	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4793939	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4793951	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62064564	0.80[EUR][1000 genomes]
rs6504340	1.00[JPT][hapmap]
rs66459980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67412921	0.90[ASN][1000 genomes]
rs7207109	1.00[JPT][hapmap]
rs8073963	1.00[JPT][hapmap]
rs8074125	1.00[JPT][hapmap]
rs8079617	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs872760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9909884	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs9912500	0.86[CEU][hapmap];1.00[JPT][hapmap];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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4793943	HOXB2	cis	Whole Blood	GTEx
rs4793943	HOXB2	cis	Adipose Subcutaneous	GTEx
rs4793943	HOXB2	cis	Thyroid	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46661600-46667000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr17:46662400-46668000	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr17:46663200-46672000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr17:46663800-46669600	Weak transcription	Pancreas	Pancrea
5	chr17:46664000-46667600	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr17:46664000-46667800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr17:46664000-46668000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr17:46664000-46670000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr17:46664600-46667000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr17:46664600-46668200	Active TSS	Rectal Smooth Muscle	rectum
11	chr17:46664800-46668200	Active TSS	NHLF	lung
12	chr17:46665200-46667400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
13	chr17:46665400-46667600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
14	chr17:46665400-46668400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr17:46665400-46668400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr17:46665400-46670000	Weak transcription	HSMMtube	muscle
17	chr17:46665600-46668000	Bivalent/Poised TSS	Fetal Lung	lung
18	chr17:46665600-46668400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr17:46665600-46672400	Active TSS	NHDF-Ad	bronchial
20	chr17:46665800-46667200	Active TSS	Colonic Mucosa	Colon
21	chr17:46665800-46667800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr17:46666000-46669600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr17:46666400-46667800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
24	chr17:46666400-46667800	Active TSS	Fetal Kidney	kidney
25	chr17:46666400-46668000	Enhancers	K562	blood
26	chr17:46666400-46669400	Weak transcription	HSMM	muscle
27	chr17:46666400-46669600	Weak transcription	Adipose Nuclei	Adipose
28	chr17:46666400-46670600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr17:46666400-46678600	Weak transcription	Hela-S3	cervix
30	chr17:46666600-46667000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
31	chr17:46666600-46667200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
32	chr17:46666600-46667400	Active TSS	Rectal Mucosa Donor 31	rectum
33	chr17:46666600-46667800	Active TSS	Colon Smooth Muscle	Colon
34	chr17:46666600-46668000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr17:46666600-46668200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
36	chr17:46666800-46667000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr17:46666800-46667000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
38	chr17:46666800-46667000	Bivalent Enhancer	GM12878-XiMat	blood
39	chr17:46666800-46667400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr17:46666800-46667400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
41	chr17:46666800-46667400	Bivalent/Poised TSS	Placenta	Placenta
42	chr17:46666800-46667400	Bivalent/Poised TSS	Small Intestine	intestine
43	chr17:46666800-46667600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr17:46666800-46668400	Weak transcription	A549	lung
45	chr17:46666800-46669200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
46	chr17:46666800-46671000	Weak transcription	HUVEC	blood vessel
47	chr17:46666800-46671600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum

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