Variant report

Variant	rs12940530
Chromosome Location	chr17:46673724-46673725
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	MAZ	chr17:46669362-46676749	IMR90	lung:	n/a	chr17:46669880-46669890 chr17:46671209-46671222 chr17:46671209-46671222 chr17:46669884-46669894 chr17:46673053-46673063
2	POLR2A	chr17:46673356-46673985	ECC-1	luminal epithelium:	n/a	n/a
3	SIN3AK20	chr17:46670331-46675986	PANC-1	pancreas:	n/a	n/a
4	CHD1	chr17:46662335-46676284	IMR90	lung:	n/a	chr17:46662455-46662465 chr17:46670083-46670093 chr17:46669891-46669901
5	ZNF263	chr17:46673661-46674035	HEK293-T-REx	kidney:	n/a	chr17:46673784-46673805
6	SUZ12	chr17:46669440-46680361	NT2-D1	testis:	n/a	n/a
7	POLR2A	chr17:46673218-46676000	ECC-1	luminal epithelium:	n/a	n/a
8	ZBTB33	chr17:46673698-46674108	K562	blood:	n/a	n/a
9	POLR2A	chr17:46673392-46675913	HEK293	kidney:	n/a	n/a
10	POLR2A	chr17:46655911-46684927	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr17:46673308-46675796	IMR90	lung:	n/a	n/a
12	TCF7L2	chr17:46673351-46674631	PANC-1	pancreas:	n/a	n/a
13	CTBP2	chr17:46673347-46675907	H1-hESC	embryonic stem cell:	n/a	n/a
14	SUZ12	chr17:46673328-46678417	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr17:46645331-46684907	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:46673414..46676816-chr17:46677264..46681067,4	MCF-7	breast:
2	chr17:46664818..46667926-chr17:46672135..46673972,3	MCF-7	breast:

Variant related genes	Relation type
HOXB-AS3	TF binding region
HOXB5	TF binding region
ENSG00000233101	Chromatin interaction
ENSG00000120093	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11079830	0.83[ASN][1000 genomes]
rs9299	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12940530	HOXB2	cis	Whole Blood	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46666400-46678600	Weak transcription	Hela-S3	cervix
2	chr17:46671000-46676200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
3	chr17:46671200-46674600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
4	chr17:46671400-46674200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr17:46671400-46674600	Bivalent Enhancer	Fetal Muscle Leg	muscle
6	chr17:46671600-46675600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr17:46671800-46674200	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr17:46671800-46676200	Weak transcription	K562	blood
9	chr17:46672000-46673800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr17:46672400-46674000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr17:46672400-46674000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr17:46672400-46674000	Flanking Bivalent TSS/Enh	Fetal Lung	lung
13	chr17:46672400-46674200	Transcr. at gene 5' and 3'	NHLF	lung
14	chr17:46672400-46674400	Bivalent Enhancer	Spleen	Spleen
15	chr17:46672400-46676800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr17:46672400-46682600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr17:46672600-46674200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr17:46672600-46674600	Strong transcription	A549	lung
19	chr17:46672600-46677000	Active TSS	Fetal Kidney	kidney
20	chr17:46672800-46674000	Strong transcription	HUVEC	blood vessel
21	chr17:46673000-46673800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
22	chr17:46673000-46673800	Weak transcription	Gastric	stomach
23	chr17:46673000-46674000	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr17:46673200-46673800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
25	chr17:46673200-46673800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
26	chr17:46673200-46673800	Bivalent Enhancer	GM12878-XiMat	blood
27	chr17:46673200-46674000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
28	chr17:46673200-46674000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
29	chr17:46673200-46674200	Bivalent Enhancer	Stomach Mucosa	stomach
30	chr17:46673200-46674800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
31	chr17:46673200-46674800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
32	chr17:46673200-46675200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr17:46673400-46673800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
34	chr17:46673400-46673800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
35	chr17:46673400-46673800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
36	chr17:46673400-46673800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr17:46673400-46673800	Flanking Active TSS	Lung	lung
38	chr17:46673400-46673800	Bivalent/Poised TSS	NHEK	skin
39	chr17:46673400-46674000	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr17:46673400-46674000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
41	chr17:46673400-46674000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr17:46673400-46674000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
43	chr17:46673400-46674000	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
44	chr17:46673400-46674000	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon
45	chr17:46673400-46674000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
46	chr17:46673400-46674000	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr17:46673400-46674000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
48	chr17:46673400-46674200	Enhancers	Pancreas	Pancrea
49	chr17:46673400-46674400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
50	chr17:46673400-46674600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood

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