Variant report

Variant	rs4793944
Chromosome Location	chr17:46667304-46667305
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	EP300	chr17:46667274-46668028	ECC-1	luminal epithelium:	n/a	n/a
2	SIN3AK20	chr17:46666419-46668321	PANC-1	pancreas:	n/a	n/a
3	REST	chr17:46667256-46667712	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr17:46667030-46667791	ECC-1	luminal epithelium:	n/a	n/a
5	CHD1	chr17:46662335-46676284	IMR90	lung:	n/a	chr17:46662455-46662465 chr17:46670083-46670093 chr17:46669891-46669901
6	POLR2A	chr17:46667116-46668037	HEK293	kidney:	n/a	n/a
7	TCF12	chr17:46667287-46667753	H1-hESC	embryonic stem cell:	n/a	n/a
8	ZNF263	chr17:46664705-46668149	HEK293-T-REx	kidney:	n/a	chr17:46667558-46667579 chr17:46667189-46667198
9	POLR2A	chr17:46667240-46668102	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr17:46655911-46684927	PANC-1	pancreas:	n/a	n/a
11	SIN3AK20	chr17:46666576-46668137	PANC-1	pancreas:	n/a	n/a
12	SUZ12	chr17:46666699-46668009	H1-hESC	embryonic stem cell:	n/a	n/a
13	TCF7L2	chr17:46666676-46668209	PANC-1	pancreas:	n/a	chr17:46668157-46668164
14	TAF1	chr17:46667294-46667745	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr17:46667150-46667339	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr17:46645331-46684907	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:46664818..46667926-chr17:46672135..46673972,3	MCF-7	breast:

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

Extended variants
information (count: 22 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs2555111	0.85[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap];0.90[LWK][hapmap];0.82[TSI][hapmap];0.80[AFR][1000 genomes];0.81[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4793944	RPRML	cis	parietal	SCAN
rs4793944	NAGLU	cis	parietal	SCAN
rs4793944	C17orf57	cis	cerebellum	SCAN
rs4793944	ACLY	cis	parietal	SCAN
rs4793944	TTLL6	cis	cerebellum	SCAN
rs4793944	PNPO	cis	parietal	SCAN
rs4793944	OSBPL7	cis	cerebellum	SCAN
rs4793944	HOXB2	cis	Whole Blood	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46662400-46668000	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr17:46663200-46672000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr17:46663800-46669600	Weak transcription	Pancreas	Pancrea
4	chr17:46664000-46667600	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr17:46664000-46667800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr17:46664000-46668000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr17:46664000-46670000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr17:46664600-46668200	Active TSS	Rectal Smooth Muscle	rectum
9	chr17:46664800-46668200	Active TSS	NHLF	lung
10	chr17:46665200-46667400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
11	chr17:46665400-46667600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr17:46665400-46668400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr17:46665400-46668400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr17:46665400-46670000	Weak transcription	HSMMtube	muscle
15	chr17:46665600-46668000	Bivalent/Poised TSS	Fetal Lung	lung
16	chr17:46665600-46668400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr17:46665600-46672400	Active TSS	NHDF-Ad	bronchial
18	chr17:46665800-46667800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr17:46666000-46669600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr17:46666400-46667800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
21	chr17:46666400-46667800	Active TSS	Fetal Kidney	kidney
22	chr17:46666400-46668000	Enhancers	K562	blood
23	chr17:46666400-46669400	Weak transcription	HSMM	muscle
24	chr17:46666400-46669600	Weak transcription	Adipose Nuclei	Adipose
25	chr17:46666400-46670600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr17:46666400-46678600	Weak transcription	Hela-S3	cervix
27	chr17:46666600-46667400	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr17:46666600-46667800	Active TSS	Colon Smooth Muscle	Colon
29	chr17:46666600-46668000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr17:46666600-46668200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
31	chr17:46666800-46667400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr17:46666800-46667400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
33	chr17:46666800-46667400	Bivalent/Poised TSS	Placenta	Placenta
34	chr17:46666800-46667400	Bivalent/Poised TSS	Small Intestine	intestine
35	chr17:46666800-46667600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr17:46666800-46668400	Weak transcription	A549	lung
37	chr17:46666800-46669200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
38	chr17:46666800-46671000	Weak transcription	HUVEC	blood vessel
39	chr17:46666800-46671600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
40	chr17:46667000-46667400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr17:46667000-46667600	Active TSS	Lung	lung
42	chr17:46667000-46667800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
43	chr17:46667200-46667400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
44	chr17:46667200-46667400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr17:46667200-46667400	Flanking Active TSS	Colonic Mucosa	Colon
46	chr17:46667200-46667400	Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr17:46667200-46667400	Enhancers	GM12878-XiMat	blood
48	chr17:46667200-46667600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
49	chr17:46667200-46667800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
50	chr17:46667200-46667800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland

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