Variant report

Variant	rs11079830
Chromosome Location	chr17:46682630-46682631
allele	A/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	POLR2A	chr17:46681190-46682711	HUVEC	blood vessel:	n/a	n/a
2	ELK1	chr17:46682234-46683132	Hela-S3	cervix:	n/a	n/a
3	TCF12	chr17:46682558-46683256	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr17:46681102-46683231	Hela-S3	cervix:	n/a	n/a
5	BCL3	chr17:46679884-46682701	A549	lung:	n/a	chr17:46682570-46682579 chr17:46682571-46682580
6	MAX	chr17:46679567-46683389	HCT-116	colon:	n/a	chr17:46682913-46682922 chr17:46680035-46680045
7	POLR2A	chr17:46682091-46682636	K562	blood:	n/a	n/a
8	USF1	chr17:46679728-46683227	HCT-116	colon:	n/a	chr17:46679897-46679913 chr17:46682399-46682410
9	TEAD4	chr17:46681728-46682723	K562	blood:	n/a	n/a
10	CEBPB	chr17:46681065-46683163	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr17:46681251-46682687	ProgFib	skin:	n/a	n/a
12	MAX	chr17:46678754-46683315	A549	lung:	n/a	chr17:46682913-46682922 chr17:46680035-46680045
13	RFX5	chr17:46679985-46683161	Hela-S3	cervix:	n/a	n/a
14	USF1	chr17:46682176-46682648	ECC-1	luminal epithelium:	n/a	chr17:46682399-46682410
15	MAX	chr17:46678862-46682704	A549	lung:	n/a	chr17:46680035-46680045
16	SP1	chr17:46680911-46682911	A549	lung:	n/a	chr17:46681776-46681788 chr17:46681777-46681787 chr17:46681776-46681788 chr17:46681752-46681766 chr17:46681777-46681787 chr17:46681777-46681791 chr17:46681777-46681786 chr17:46681778-46681787
17	TCF12	chr17:46682558-46683266	ECC-1	luminal epithelium:	n/a	n/a
18	USF1	chr17:46681178-46682683	A549	lung:	n/a	chr17:46682399-46682410
19	POLR2A	chr17:46681074-46683297	HUVEC	blood vessel:	n/a	n/a
20	MAX	chr17:46682231-46683217	Hela-S3	cervix:	n/a	chr17:46682913-46682922
21	USF1	chr17:46682052-46682707	A549	lung:	n/a	chr17:46682399-46682410
22	USF2	chr17:46681328-46682686	Hela-S3	cervix:	n/a	chr17:46682398-46682409
23	YY1	chr17:46682214-46682768	K562	blood:	n/a	chr17:46682535-46682545
24	POLR2A	chr17:46680629-46683289	Hela-S3	cervix:	n/a	n/a
25	NFYB	chr17:46682259-46682649	K562	blood:	n/a	n/a
26	MAZ	chr17:46681199-46683119	Hela-S3	cervix:	n/a	chr17:46682913-46682922
27	TBP	chr17:46680455-46683270	Hela-S3	cervix:	n/a	n/a
28	MAX	chr17:46680018-46683250	Hela-S3	cervix:	n/a	chr17:46682913-46682922 chr17:46680035-46680045
29	YY1	chr17:46680944-46682830	A549	lung:	n/a	chr17:46682535-46682545
30	ATF3	chr17:46681144-46682645	A549	lung:	n/a	n/a
31	POLR2A	chr17:46680931-46683223	Hela-S3	cervix:	n/a	n/a
32	USF1	chr17:46681090-46682726	A549	lung:	n/a	chr17:46682399-46682410
33	BCL3	chr17:46679714-46683211	A549	lung:	n/a	chr17:46682570-46682579 chr17:46682571-46682580
34	RCOR1	chr17:46681218-46682679	Hela-S3	cervix:	n/a	n/a
35	SIN3AK20	chr17:46680927-46683261	PANC-1	pancreas:	n/a	n/a
36	TCF7L2	chr17:46682257-46683061	Hela-S3	cervix:	n/a	n/a
37	TAF1	chr17:46680611-46682787	A549	lung:	n/a	n/a
38	POLR2A	chr17:46680536-46682652	HUVEC	blood vessel:	n/a	n/a
39	USF2	chr17:46682232-46682685	K562	blood:	n/a	chr17:46682398-46682409
40	RCOR1	chr17:46682099-46683203	K562	blood:	n/a	n/a
41	NFIC	chr17:46682595-46683348	ECC-1	luminal epithelium:	n/a	chr17:46682969-46682986 chr17:46682970-46682986
42	POLR2A	chr17:46681229-46683202	Hela-S3	cervix:	n/a	n/a
43	ZKSCAN1	chr17:46682623-46683198	Hela-S3	cervix:	n/a	n/a
44	YY1	chr17:46682344-46683111	ECC-1	luminal epithelium:	n/a	chr17:46682535-46682545
45	TAF1	chr17:46682096-46682679	Hela-S3	cervix:	n/a	n/a
46	USF1	chr17:46682119-46682676	ECC-1	luminal epithelium:	n/a	chr17:46682399-46682410
47	POLR2A	chr17:46681042-46683164	K562	blood:	n/a	n/a
48	POLR2A	chr17:46682079-46683154	HCT-116	colon:	n/a	n/a
49	USF1	chr17:46682093-46682666	A549	lung:	n/a	chr17:46682399-46682410
50	POLR2A	chr17:46681010-46682636	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46622432..46624034-chr17:46681830..46683830,2	K562	blood:
2	chr17:46675371..46683952-chr17:46685648..46690575,16	MCF-7	breast:
3	chr17:46662731..46663402-chr17:46682480..46683122,2	K562	blood:
4	chr17:46679267..46681075-chr17:46682371..46684611,3	MCF-7	breast:

Variant related genes	Relation type
HOXB3	TF binding region
HOXB6	TF binding region
ENSG00000233101	Chromatin interaction
ENSG00000260027	Chromatin interaction
ENSG00000173917	Chromatin interaction
ENSG00000230148	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12940530	0.83[ASN][1000 genomes]
rs2303486	0.81[CEU][hapmap]
rs2740760	0.86[JPT][hapmap]
rs9299	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.98[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11079830	HOXB2	cis	Whole Blood	GTEx
rs11079830	PNPO	cis	parietal	SCAN
rs11079830	TTLL6	cis	cerebellum	SCAN
rs11079830	RUNDC3A	cis	parietal	SCAN
rs11079830	HOXB2	cis	multi-tissue	Pritchard
rs11079830	COASY	cis	parietal	SCAN
rs11079830	MPP2	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46677400-46684000	Active TSS	Fetal Kidney	kidney
2	chr17:46680200-46683000	Bivalent/Poised TSS	Psoas Muscle	Psoas
3	chr17:46680400-46682800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
4	chr17:46680400-46682800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
5	chr17:46680800-46682800	Active TSS	Colon Smooth Muscle	Colon
6	chr17:46681000-46683000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
7	chr17:46681200-46682800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr17:46681200-46686000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr17:46681800-46684600	Active TSS	Colonic Mucosa	Colon
10	chr17:46681800-46686400	Weak transcription	GM12878-XiMat	blood
11	chr17:46682000-46683000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr17:46682200-46683200	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr17:46682200-46683200	Flanking Active TSS	HUVEC	blood vessel
14	chr17:46682400-46682800	Bivalent Enhancer	NHEK	skin
15	chr17:46682400-46683000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr17:46682400-46683200	Flanking Active TSS	A549	lung
17	chr17:46682400-46683400	Weak transcription	NHLF	lung
18	chr17:46682400-46684400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr17:46682600-46682800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr17:46682600-46682800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
21	chr17:46682600-46682800	Flanking Active TSS	HSMMtube	muscle
22	chr17:46682600-46683000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr17:46682600-46683000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr17:46682600-46683000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr17:46682600-46683000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr17:46682600-46683000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
27	chr17:46682600-46683000	Bivalent Enhancer	Fetal Muscle Leg	muscle
28	chr17:46682600-46683000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
29	chr17:46682600-46683000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr17:46682600-46683000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
31	chr17:46682600-46683000	Flanking Active TSS	HSMM	muscle
32	chr17:46682600-46683000	Flanking Active TSS	K562	blood
33	chr17:46682600-46683000	Flanking Active TSS	NHDF-Ad	bronchial
34	chr17:46682600-46683200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr17:46682600-46683400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
36	chr17:46682600-46683600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr17:46682600-46683600	Flanking Active TSS	Hela-S3	cervix

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