Variant report

Variant	rs4793589
Chromosome Location	chr17:46667863-46667864
allele	C/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	EP300	chr17:46667274-46668028	ECC-1	luminal epithelium:	n/a	n/a
2	SIN3AK20	chr17:46666419-46668321	PANC-1	pancreas:	n/a	n/a
3	CTCF	chr17:46667840-46667990	AG04449	skin:	n/a	n/a
4	TEAD4	chr17:46667438-46667882	ECC-1	luminal epithelium:	n/a	n/a
5	ESR1	chr17:46667466-46667942	ECC-1	luminal epithelium:	n/a	n/a
6	ESR1	chr17:46667489-46668002	ECC-1	luminal epithelium:	n/a	n/a
7	USF1	chr17:46667411-46667933	ECC-1	luminal epithelium:	n/a	chr17:46667679-46667688 chr17:46667679-46667688 chr17:46667673-46667694 chr17:46667680-46667689 chr17:46667677-46667690
8	POLR2A	chr17:46667567-46668068	Hela-S3	cervix:	n/a	n/a
9	ESR1	chr17:46667495-46667920	ECC-1	luminal epithelium:	n/a	n/a
10	CHD1	chr17:46662335-46676284	IMR90	lung:	n/a	chr17:46662455-46662465 chr17:46670083-46670093 chr17:46669891-46669901
11	POLR2A	chr17:46667116-46668037	HEK293	kidney:	n/a	n/a
12	POLR2A	chr17:46667387-46667918	Gliobla	brain:	n/a	n/a
13	KAP1	chr17:46667434-46668115	HEK293	kidney:	n/a	n/a
14	TCF7L2	chr17:46667478-46668154	HEK293	kidney:	n/a	n/a
15	ZNF263	chr17:46664705-46668149	HEK293-T-REx	kidney:	n/a	chr17:46667558-46667579 chr17:46667189-46667198
16	REST	chr17:46667773-46668138	PANC-1	pancreas:	n/a	chr17:46667977-46667990
17	POLR2A	chr17:46667240-46668102	ECC-1	luminal epithelium:	n/a	n/a
18	KAP1	chr17:46667507-46668027	U2OS	brain:	n/a	n/a
19	POLR2A	chr17:46655911-46684927	PANC-1	pancreas:	n/a	n/a
20	SIN3AK20	chr17:46666576-46668137	PANC-1	pancreas:	n/a	n/a
21	SUZ12	chr17:46666699-46668009	H1-hESC	embryonic stem cell:	n/a	n/a
22	TCF7L2	chr17:46666676-46668209	PANC-1	pancreas:	n/a	chr17:46668157-46668164
23	CTBP2	chr17:46667370-46668059	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr17:46667396-46668132	ProgFib	skin:	n/a	n/a
25	USF1	chr17:46667367-46667971	ECC-1	luminal epithelium:	n/a	chr17:46667679-46667688 chr17:46667679-46667688 chr17:46667673-46667694 chr17:46667680-46667689 chr17:46667677-46667690
26	POLR2A	chr17:46645331-46684907	PANC-1	pancreas:	n/a	n/a

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CALCOCO2-8	chr17:46667823-46667951	NONHSAT054433
2	lnc-CALCOCO2-8	chr17:46667839-46667951	ENSG00000233101.6
3	lnc-CALCOCO2-8	chr17:46667782-46667951	ENSG00000233101.6
4	lnc-CALCOCO2-8	chr17:46667804-46667951	ENSG00000233101.6
5	lnc-CALCOCO2-8	chr17:46667782-46667951	NR_033201
6	lnc-CALCOCO2-8	chr17:46667843-46667951	ENSG00000233101.6
7	lnc-CALCOCO2-8	chr17:46667782-46667951	NR_110331
8	lnc-CALCOCO2-8	chr17:46667782-46667951	NR_033202
9	lnc-CALCOCO2-8	chr17:46667842-46667951	NONHSAT054434

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

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1062037	0.90[ASN][1000 genomes]
rs1123630	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]
rs12952262	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1529334	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
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]
rs35624684	0.83[EUR][1000 genomes]
rs35825473	0.90[ASN][1000 genomes]
rs4646993	0.90[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]
rs4793943	1.00[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]
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]
rs872760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9912500	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
rs4793589	HOXB2	cis	Whole Blood	GTEx
rs4793589	HOXB2	cis	Adipose Subcutaneous	GTEx
rs4793589	HOXB2	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46662400-46668000	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr17:46663200-46672000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr17:46663800-46669600	Weak transcription	Pancreas	Pancrea
4	chr17:46664000-46668000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr17:46664000-46670000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr17:46664600-46668200	Active TSS	Rectal Smooth Muscle	rectum
7	chr17:46664800-46668200	Active TSS	NHLF	lung
8	chr17:46665400-46668400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr17:46665400-46668400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr17:46665400-46670000	Weak transcription	HSMMtube	muscle
11	chr17:46665600-46668000	Bivalent/Poised TSS	Fetal Lung	lung
12	chr17:46665600-46668400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr17:46665600-46672400	Active TSS	NHDF-Ad	bronchial
14	chr17:46666000-46669600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr17:46666400-46668000	Enhancers	K562	blood
16	chr17:46666400-46669400	Weak transcription	HSMM	muscle
17	chr17:46666400-46669600	Weak transcription	Adipose Nuclei	Adipose
18	chr17:46666400-46670600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr17:46666400-46678600	Weak transcription	Hela-S3	cervix
20	chr17:46666600-46668000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr17:46666600-46668200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
22	chr17:46666800-46668400	Weak transcription	A549	lung
23	chr17:46666800-46669200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
24	chr17:46666800-46671000	Weak transcription	HUVEC	blood vessel
25	chr17:46666800-46671600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
26	chr17:46667200-46668200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
27	chr17:46667400-46668000	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr17:46667400-46668600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr17:46667600-46668000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
30	chr17:46667600-46668000	Bivalent Enhancer	HepG2	liver
31	chr17:46667600-46668200	Bivalent/Poised TSS	Fetal Brain Male	brain
32	chr17:46667600-46668200	Enhancers	GM12878-XiMat	blood
33	chr17:46667600-46668400	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr17:46667600-46668600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr17:46667600-46669400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr17:46667800-46668000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
37	chr17:46667800-46668000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr17:46667800-46668000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr17:46667800-46668000	Active TSS	Colonic Mucosa	Colon
40	chr17:46667800-46668000	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
41	chr17:46667800-46668000	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr17:46667800-46668200	Flanking Active TSS	Fetal Kidney	kidney
43	chr17:46667800-46668200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
44	chr17:46667800-46668200	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr17:46667800-46668400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr17:46667800-46668800	Flanking Active TSS	Colon Smooth Muscle	Colon
47	chr17:46667800-46669400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

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