Variant report

Variant	rs12939324
Chromosome Location	chr17:46687752-46687753
allele	A/C
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	EGR1	chr17:46687467-46687822	K562	blood:	n/a	chr17:46687614-46687627 chr17:46687617-46687627
2	EP300	chr17:46687607-46688037	ECC-1	luminal epithelium:	n/a	n/a
3	PML	chr17:46687581-46688690	GM12878	blood:	n/a	n/a
4	E2F6	chr17:46687436-46688997	A549	lung:	n/a	chr17:46687709-46687718 chr17:46687918-46687930 chr17:46687619-46687628 chr17:46687785-46687800
5	SUZ12	chr17:46686802-46688344	NT2-D1	testis:	n/a	n/a
6	POLR2A	chr17:46687386-46688986	HCT-116	colon:	n/a	n/a
7	SP1	chr17:46687602-46688986	A549	lung:	n/a	chr17:46687618-46687630 chr17:46688409-46688418 chr17:46687708-46687720 chr17:46687710-46687719 chr17:46688410-46688419 chr17:46687710-46687719 chr17:46688409-46688419 chr17:46688408-46688420 chr17:46688408-46688420 chr17:46688409-46688419 chr17:46687620-46687629 chr17:46688409-46688418 chr17:46687619-46687628 chr17:46687794-46687801 chr17:46687705-46687719 chr17:46687709-46687718
8	HEY1	chr17:46687576-46688201	K562	blood:	n/a	n/a
9	MAX	chr17:46687345-46689850	A549	lung:	n/a	chr17:46689596-46689606 chr17:46687379-46687389 chr17:46688399-46688412 chr17:46688400-46688411 chr17:46688415-46688424 chr17:46687617-46687627 chr17:46688401-46688410 chr17:46688401-46688410 chr17:46688413-46688422 chr17:46688414-46688425 chr17:46689593-46689603 chr17:46688401-46688410 chr17:46688399-46688412 chr17:46688400-46688409
10	POLR2A	chr17:46687211-46689612	ProgFib	skin:	n/a	n/a
11	ELF1	chr17:46687463-46688907	MCF-7	breast:	n/a	chr17:46687838-46687850
12	POLR2A	chr17:46687590-46688210	GM12878	blood:	n/a	n/a
13	POLR2A	chr17:46687477-46689378	HUVEC	blood vessel:	n/a	n/a
14	TAF1	chr17:46687346-46688984	A549	lung:	n/a	n/a
15	POLR2A	chr17:46687624-46688859	Raji	blood:	n/a	n/a
16	MAX	chr17:46687514-46688778	Hela-S3	cervix:	n/a	chr17:46688399-46688412 chr17:46688400-46688411 chr17:46688415-46688424 chr17:46687617-46687627 chr17:46688401-46688410 chr17:46688401-46688410 chr17:46688413-46688422 chr17:46688414-46688425 chr17:46688401-46688410 chr17:46688399-46688412 chr17:46688400-46688409
17	PAX5	chr17:46687606-46687872	GM12878	blood:	n/a	n/a
18	POLR2A	chr17:46687601-46688549	GM12878	blood:	n/a	n/a
19	USF1	chr17:46687436-46689840	HCT-116	colon:	n/a	chr17:46688414-46688425 chr17:46688565-46688581 chr17:46688400-46688411
20	POLR2A	chr17:46687462-46688390	GM12892	blood:	n/a	n/a
21	POLR2A	chr17:46687562-46688622	GM12878	blood:	n/a	n/a
22	JUND	chr17:46687507-46688800	A549	lung:	n/a	n/a
23	TAF1	chr17:46687624-46688175	Hela-S3	cervix:	n/a	n/a
24	FOSL2	chr17:46686907-46687832	A549	lung:	n/a	chr17:46687359-46687368
25	YY1	chr17:46687476-46688225	K562	blood:	n/a	chr17:46687709-46687718
26	MYC	chr17:46687672-46687814	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr17:46687612-46688164	A549	lung:	n/a	n/a
28	ELK1	chr17:46687716-46688548	Hela-S3	cervix:	n/a	n/a
29	GABPA	chr17:46687635-46688121	A549	lung:	n/a	chr17:46687709-46687718
30	SIN3AK20	chr17:46687005-46689014	PANC-1	pancreas:	n/a	n/a
31	POLR2A	chr17:46686211-46690442	SK-N-MC	brain:	n/a	n/a
32	POLR2A	chr17:46687586-46688196	A549	lung:	n/a	n/a
33	E2F1	chr17:46687685-46688267	Hela-S3	cervix:	n/a	chr17:46687709-46687718 chr17:46687918-46687930 chr17:46687947-46687958 chr17:46687785-46687800
34	POLR2A	chr17:46687564-46688201	GM12878	blood:	n/a	n/a
35	POLR2A	chr17:46687368-46688803	HUVEC	blood vessel:	n/a	n/a
36	MAX	chr17:46687054-46691101	A549	lung:	n/a	chr17:46689596-46689606 chr17:46687379-46687389 chr17:46688399-46688412 chr17:46688400-46688411 chr17:46688415-46688424 chr17:46687617-46687627 chr17:46688401-46688410 chr17:46688401-46688410 chr17:46688413-46688422 chr17:46688414-46688425 chr17:46689593-46689603 chr17:46688401-46688410 chr17:46688399-46688412 chr17:46687253-46687263 chr17:46688400-46688409
37	YY1	chr17:46687534-46688617	GM12878	blood:	n/a	chr17:46687709-46687718 chr17:46688427-46688436 chr17:46688546-46688557
38	HA-E2F1	chr17:46687654-46688410	MCF-7	breast:	n/a	chr17:46687709-46687718 chr17:46687947-46687958 chr17:46687785-46687800
39	ELF1	chr17:46687595-46688090	K562	blood:	n/a	chr17:46687838-46687850
40	ELF1	chr17:46687502-46688203	GM12878	blood:	n/a	chr17:46687838-46687850
41	TCF12	chr17:46687577-46687987	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr17:46687550-46688788	K562	blood:	n/a	n/a
43	HA-E2F1	chr17:46687608-46688307	Hela-S3	cervix:	n/a	chr17:46687709-46687718 chr17:46687619-46687628 chr17:46687947-46687958 chr17:46687785-46687800
44	TAF1	chr17:46687506-46688688	ECC-1	luminal epithelium:	n/a	n/a
45	TCF12	chr17:46687095-46690958	A549	lung:	n/a	chr17:46687150-46687157 chr17:46689250-46689260
46	REST	chr17:46687724-46688261	PANC-1	pancreas:	n/a	n/a
47	EGR1	chr17:46687480-46687856	K562	blood:	n/a	chr17:46687614-46687627 chr17:46687617-46687627
48	MTA3	chr17:46687151-46688965	GM12878	blood:	n/a	n/a
49	POLR2A	chr17:46687582-46688001	GM12891	blood:	n/a	n/a
50	RCOR1	chr17:46687749-46688889	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:62608963..62609484-chr17:46687712..46688537,2	Hela-S3	cervix:
2	chr17:46212650..46214229-chr17:46686261..46688122,2	MCF-7	breast:
3	chr17:46687246..46688797-chr17:46690963..46692920,2	MCF-7	breast:
4	chr16:30388745..30389618-chr17:46687637..46688159,2	Hela-S3	cervix:
5	chr17:46687373..46688200-chrX:48660448..48661193,2	Hela-S3	cervix:
6	chr17:46685746..46689281-chr17:46702801..46705653,3	MCF-7	breast:
7	chr17:46412297..46414059-chr17:46686711..46688269,2	MCF-7	breast:
8	chr17:46337445..46339514-chr17:46686634..46688158,2	MCF-7	breast:
9	chr17:46675371..46683952-chr17:46685648..46690575,16	MCF-7	breast:
10	chr17:46687211..46688141-chr20:30181460..30182033,2	HCT-116	colon:
11	chr17:46686493..46690300-chr17:46702976..46707350,6	MCF-7	breast:

Variant related genes	Relation type
HOXB7	TF binding region
ENSG00000133316	Chromatin interaction
ENSG00000170689	Chromatin interaction
ENSG00000242207	Chromatin interaction
ENSG00000233101	Chromatin interaction
ENSG00000180035	Chromatin interaction
ENSG00000108511	Chromatin interaction
ENSG00000120093	Chromatin interaction
ENSG00000094631	Chromatin interaction
ENSG00000180209	Chromatin interaction
ENSG00000120068	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1123630	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12952262	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28575348	0.90[EUR][1000 genomes]
rs4646993	0.90[EUR][1000 genomes]
rs4793589	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4793938	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4793939	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4793943	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4793951	0.83[EUR][1000 genomes]
rs66459980	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs872760	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9896015	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9909884	0.90[EUR][1000 genomes]
rs9912500	0.90[EUR][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	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	nsv543380	chr17:46686151-46721371	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12939324	HOXB2	cis	Adipose Subcutaneous	GTEx
rs12939324	HOXB2	cis	Whole Blood	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46683600-46691000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr17:46686200-46687800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr17:46686200-46688200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr17:46687000-46688600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
5	chr17:46687000-46689000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr17:46687000-46689000	Active TSS	Fetal Kidney	kidney
7	chr17:46687000-46690400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
8	chr17:46687000-46691600	Active TSS	HSMMtube	muscle
9	chr17:46687200-46687800	Bivalent Enhancer	Primary B cells from cord blood	blood
10	chr17:46687200-46687800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
11	chr17:46687200-46687800	Bivalent/Poised TSS	Psoas Muscle	Psoas
12	chr17:46687200-46687800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
13	chr17:46687200-46688600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr17:46687200-46688600	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
15	chr17:46687200-46688600	Active TSS	NHLF	lung
16	chr17:46687200-46688800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
17	chr17:46687200-46689000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
18	chr17:46687200-46689000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
19	chr17:46687200-46689200	Active TSS	Right Atrium	heart
20	chr17:46687200-46689200	Active TSS	Hela-S3	cervix
21	chr17:46687200-46689200	Active TSS	HSMM	muscle
22	chr17:46687200-46689600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
23	chr17:46687200-46690400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
24	chr17:46687200-46692800	Active TSS	NHDF-Ad	bronchial
25	chr17:46687400-46687800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr17:46687400-46687800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
27	chr17:46687400-46687800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
28	chr17:46687400-46687800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
29	chr17:46687400-46687800	Bivalent/Poised TSS	Right Ventricle	heart
30	chr17:46687400-46687800	Bivalent/Poised TSS	NHEK	skin
31	chr17:46687400-46688000	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
32	chr17:46687400-46688000	Flanking Bivalent TSS/Enh	Ovary	ovary
33	chr17:46687400-46688000	Bivalent Enhancer	Stomach Mucosa	stomach
34	chr17:46687400-46688000	Active TSS	GM12878-XiMat	blood
35	chr17:46687400-46688000	Active TSS	HUVEC	blood vessel
36	chr17:46687400-46688200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
37	chr17:46687400-46688200	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
38	chr17:46687400-46688200	Bivalent Enhancer	Fetal Brain Male	brain
39	chr17:46687400-46688400	Flanking Bivalent TSS/Enh	HepG2	liver
40	chr17:46687400-46688600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr17:46687400-46688600	Active TSS	Small Intestine	intestine
42	chr17:46687400-46688800	Flanking Bivalent TSS/Enh	Thymus	Thymus
43	chr17:46687400-46689000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
44	chr17:46687400-46689000	Active TSS	Aorta	Aorta
45	chr17:46687400-46689000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
46	chr17:46687400-46689000	Flanking Bivalent TSS/Enh	Placenta	Placenta
47	chr17:46687400-46689000	Active TSS	Rectal Smooth Muscle	rectum
48	chr17:46687400-46689200	Bivalent/Poised TSS	Fetal Lung	lung
49	chr17:46687400-46689200	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr17:46687400-46689200	Active TSS	Sigmoid Colon	Sigmoid Colon

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