Variant report

Variant	rs4793938
Chromosome Location	chr17:46665229-46665230
allele	G/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	FOXA1	chr17:46664914-46665251	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr17:46664785-46665552	ECC-1	luminal epithelium:	n/a	n/a
3	TCF12	chr17:46664776-46665347	ECC-1	luminal epithelium:	n/a	chr17:46665088-46665095
4	SIN3AK20	chr17:46664679-46666172	PANC-1	pancreas:	n/a	n/a
5	REST	chr17:46664861-46665419	A549	lung:	n/a	chr17:46664948-46664956
6	TCF12	chr17:46664693-46665561	ECC-1	luminal epithelium:	n/a	chr17:46665440-46665450 chr17:46665088-46665095
7	TEAD4	chr17:46664789-46665388	ECC-1	luminal epithelium:	n/a	n/a
8	TCF12	chr17:46664702-46665472	A549	lung:	n/a	chr17:46665440-46665450 chr17:46665088-46665095
9	CHD1	chr17:46662335-46676284	IMR90	lung:	n/a	chr17:46662455-46662465 chr17:46670083-46670093 chr17:46669891-46669901
10	EP300	chr17:46664775-46665575	ECC-1	luminal epithelium:	n/a	chr17:46665051-46665065
11	ZNF263	chr17:46664705-46668149	HEK293-T-REx	kidney:	n/a	chr17:46667558-46667579 chr17:46667189-46667198
12	KAP1	chr17:46664760-46665325	U2OS	brain:	n/a	n/a
13	FOXA2	chr17:46664902-46665422	A549	lung:	n/a	n/a
14	POLR2A	chr17:46665221-46665267	HUVEC	blood vessel:	n/a	n/a
15	TCF7L2	chr17:46664773-46665420	PANC-1	pancreas:	n/a	n/a
16	FOXA2	chr17:46664879-46665354	A549	lung:	n/a	n/a
17	POLR2A	chr17:46655911-46684927	PANC-1	pancreas:	n/a	n/a
18	FOXM1	chr17:46664731-46665498	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr17:46665150-46665607	ECC-1	luminal epithelium:	n/a	n/a
20	SIN3AK20	chr17:46664815-46665508	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr17:46664727-46665358	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr17:46645331-46684907	PANC-1	pancreas:	n/a	n/a
23	EP300	chr17:46664801-46665368	ECC-1	luminal epithelium:	n/a	chr17:46665051-46665065

No.	Distal block	Cell Line	Cell type
1	chr17:46664818..46667926-chr17:46672135..46673972,3	MCF-7	breast:
2	chr17:46663918..46665651-chr17:46666465..46668696,2	K562	blood:
3	chr17:46335792..46337533-chr17:46664070..46666326,2	K562	blood:
4	chr17:46663028..46666157-chr17:46668975..46671535,3	MCF-7	breast:

Variant related genes	Relation type
HOXB-AS3	TF binding region
ENSG00000233101	Chromatin interaction
ENSG00000120075	Chromatin interaction
ENSG00000120093	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	0.84[ASN][1000 genomes]
rs1123630	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12939324	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12952262	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1529334	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3087996	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34490194	0.80[EUR][1000 genomes]
rs34527992	0.80[EUR][1000 genomes]
rs34822124	0.80[EUR][1000 genomes]
rs35624684	0.83[EUR][1000 genomes]
rs35825473	0.84[ASN][1000 genomes]
rs4646993	0.84[ASN][1000 genomes]
rs4793589	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4793939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4793943	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4793951	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62064564	0.80[EUR][1000 genomes]
rs66459980	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67412921	0.84[ASN][1000 genomes]
rs872760	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9912500	0.84[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
rs4793938	HOXB2	cis	Thyroid	GTEx
rs4793938	HOXB2	cis	Adipose Subcutaneous	GTEx
rs4793938	HOXB2	cis	Whole Blood	GTEx

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

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	chr17:46662400-46665600	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr17:46662400-46668000	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr17:46663200-46665400	Flanking Active TSS	Colonic Mucosa	Colon
6	chr17:46663200-46672000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr17:46663400-46666400	Enhancers	Lung	lung
8	chr17:46663600-46665800	Weak transcription	K562	blood
9	chr17:46663800-46665400	Enhancers	Muscle Satellite Cultured Cells	--
10	chr17:46663800-46665400	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr17:46663800-46665600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
12	chr17:46663800-46665600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
13	chr17:46663800-46665600	Bivalent Enhancer	Liver	Liver
14	chr17:46663800-46665800	Enhancers	Spleen	Spleen
15	chr17:46663800-46666800	Enhancers	A549	lung
16	chr17:46663800-46669600	Weak transcription	Pancreas	Pancrea
17	chr17:46664000-46665600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr17:46664000-46665600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
19	chr17:46664000-46666400	Enhancers	HSMM	muscle
20	chr17:46664000-46666600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr17:46664000-46667600	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr17:46664000-46667800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
23	chr17:46664000-46668000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr17:46664000-46670000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr17:46664200-46665600	Flanking Bivalent TSS/Enh	Fetal Lung	lung
26	chr17:46664200-46666000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
27	chr17:46664200-46666800	Enhancers	HUVEC	blood vessel
28	chr17:46664400-46665400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr17:46664400-46665400	Enhancers	HSMMtube	muscle
30	chr17:46664400-46666000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr17:46664400-46666400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr17:46664400-46666800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
33	chr17:46664600-46665400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr17:46664600-46665600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr17:46664600-46665600	Flanking Active TSS	NHDF-Ad	bronchial
36	chr17:46664600-46666400	Enhancers	Hela-S3	cervix
37	chr17:46664600-46667000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr17:46664600-46668200	Active TSS	Rectal Smooth Muscle	rectum
39	chr17:46664800-46665600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
40	chr17:46664800-46665800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr17:46664800-46666800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
42	chr17:46664800-46668200	Active TSS	NHLF	lung
43	chr17:46665000-46665600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
44	chr17:46665000-46665600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
45	chr17:46665000-46666200	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr17:46665200-46665400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
47	chr17:46665200-46665400	Active TSS	Fetal Kidney	kidney
48	chr17:46665200-46665800	Flanking Active TSS	Colon Smooth Muscle	Colon
49	chr17:46665200-46665800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
50	chr17:46665200-46667400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach

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