Variant report

Variant	rs1123630
Chromosome Location	chr17:46671816-46671817
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	SIN3AK20	chr17:46670500-46672191	PANC-1	pancreas:	n/a	n/a
5	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
6	CTBP2	chr17:46671319-46673025	H1-hESC	embryonic stem cell:	n/a	n/a
7	SUZ12	chr17:46670436-46673044	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr17:46670920-46671829	A549	lung:	n/a	chr17:46671401-46671414 chr17:46671400-46671416 chr17:46671399-46671417
9	SIN3AK20	chr17:46670331-46675986	PANC-1	pancreas:	n/a	n/a
10	KAP1	chr17:46671567-46671996	U2OS	brain:	n/a	n/a
11	REST	chr17:46671298-46671888	A549	lung:	n/a	n/a
12	CHD1	chr17:46662335-46676284	IMR90	lung:	n/a	chr17:46662455-46662465 chr17:46670083-46670093 chr17:46669891-46669901
13	CTCF	chr17:46670500-46671977	SK-N-SH	brain:	n/a	chr17:46671401-46671414 chr17:46671400-46671416 chr17:46671399-46671417
14	SUZ12	chr17:46669440-46680361	NT2-D1	testis:	n/a	n/a
15	MXI1	chr17:46670335-46673027	IMR90	lung:	n/a	n/a
16	JUND	chr17:46671162-46671960	A549	lung:	n/a	chr17:46671173-46671182
17	TCF7L2	chr17:46671229-46672791	PANC-1	pancreas:	n/a	chr17:46671659-46671673 chr17:46671661-46671670
18	TCF12	chr17:46671190-46672199	A549	lung:	n/a	n/a
19	ZNF263	chr17:46671257-46671980	HEK293-T-REx	kidney:	n/a	chr17:46671346-46671367
20	POLR2A	chr17:46670404-46672018	ECC-1	luminal epithelium:	n/a	n/a
21	BCL3	chr17:46671083-46672083	A549	lung:	n/a	chr17:46671771-46671780 chr17:46671830-46671838
22	RAD21	chr17:46671002-46671828	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr17:46671117-46672132	SK-N-MC	brain:	n/a	n/a
24	POLR2A	chr17:46655911-46684927	PANC-1	pancreas:	n/a	n/a
25	FOSL2	chr17:46671218-46671959	A549	lung:	n/a	n/a
26	EP300	chr17:46670616-46671914	ECC-1	luminal epithelium:	n/a	chr17:46671847-46671863
27	CTCF	chr17:46671700-46671850	HVMF	connective:	n/a	n/a
28	POLR2A	chr17:46671287-46671833	HUVEC	blood vessel:	n/a	n/a
29	CTCF	chr17:46671700-46671850	GM12868	blood:	n/a	n/a
30	POLR2A	chr17:46671195-46673088	ECC-1	luminal epithelium:	n/a	n/a
31	TCF7L2	chr17:46671367-46671990	HEK293	kidney:	n/a	chr17:46671659-46671673 chr17:46671661-46671670
32	KAP1	chr17:46671297-46671980	HEK293	kidney:	n/a	n/a
33	POLR2A	chr17:46670513-46672579	IMR90	lung:	n/a	n/a
34	POLR2A	chr17:46645331-46684907	PANC-1	pancreas:	n/a	n/a
35	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
HOXB3	TF binding region
HOXB-AS3	TF binding region
HOXB5	TF binding region
ENSG00000141293	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1062037	0.86[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	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1529334	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]
rs2229302	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs3087996	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34490194	0.80[EUR][1000 genomes]
rs34527992	0.80[EUR][1000 genomes]
rs34822124	0.80[EUR][1000 genomes]
rs35621842	0.80[CEU][hapmap]
rs35624684	0.83[EUR][1000 genomes]
rs35825473	0.86[ASN][1000 genomes]
rs4239158	0.87[CEU][hapmap]
rs4646993	0.86[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4793589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4793938	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4793939	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4793943	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]
rs4793951	0.87[EUR][1000 genomes];0.93[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];1.00[ASN][1000 genomes]
rs67412921	0.86[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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9909884	0.87[CEU][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9912500	0.86[CEU][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.93[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1123630	HOXB2	cis	multi-tissue	Pritchard
rs1123630	HOXB2	cis	Whole Blood	GTEx
rs1123630	HOXB2	cis	Thyroid	GTEx
rs1123630	HOXB2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:58 , 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	chr17:46670000-46672000	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr17:46670000-46672200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr17:46671000-46672000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
11	chr17:46671000-46672000	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr17:46671000-46672400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr17:46671000-46672600	Enhancers	HUVEC	blood vessel
14	chr17:46671000-46673400	Weak transcription	Pancreas	Pancrea
15	chr17:46671000-46676200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
16	chr17:46671200-46672000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr17:46671200-46673000	Genic enhancers	Rectal Mucosa Donor 31	rectum
18	chr17:46671200-46674600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr17:46671400-46672000	Flanking Bivalent TSS/Enh	Fetal Lung	lung
20	chr17:46671400-46672000	Bivalent/Poised TSS	HepG2	liver
21	chr17:46671400-46672000	Enhancers	HSMMtube	muscle
22	chr17:46671400-46673600	Weak transcription	Right Atrium	heart
23	chr17:46671400-46674200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr17:46671400-46674600	Bivalent Enhancer	Fetal Muscle Leg	muscle
25	chr17:46671600-46672000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
26	chr17:46671600-46672000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
27	chr17:46671600-46672000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
28	chr17:46671600-46672000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
29	chr17:46671600-46672000	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
30	chr17:46671600-46672000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
31	chr17:46671600-46672200	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
32	chr17:46671600-46672200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr17:46671600-46672200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
34	chr17:46671600-46672600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr17:46671600-46672600	Flanking Active TSS	Colon Smooth Muscle	Colon
36	chr17:46671600-46672800	Bivalent Enhancer	Placenta	Placenta
37	chr17:46671600-46673000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
38	chr17:46671600-46673600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
39	chr17:46671600-46675600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr17:46671800-46672000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr17:46671800-46672000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
42	chr17:46671800-46672000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr17:46671800-46672000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr17:46671800-46672000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr17:46671800-46672000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr17:46671800-46672000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
47	chr17:46671800-46672000	Flanking Active TSS	HSMM	muscle
48	chr17:46671800-46672000	Flanking Bivalent TSS/Enh	NH-A	brain
49	chr17:46671800-46672200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr17:46671800-46672200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell

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