Variant report

Variant	rs999493
Chromosome Location	chr17:46625519-46625520
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	POLR2A	chr17:46620117-46628421	PANC-1	pancreas:	n/a	n/a
2	KAP1	chr17:46623982-46625541	HEK293	kidney:	n/a	n/a
3	POLR2A	chr17:46616545-46629919	PANC-1	pancreas:	n/a	n/a
4	RCOR1	chr17:46625197-46626340	K562	blood:	n/a	n/a
5	MAX	chr17:46625219-46625947	K562	blood:	n/a	n/a
6	POLR2A	chr17:46623587-46626234	K562	blood:	n/a	n/a
7	NR2F2	chr17:46624977-46626099	K562	blood:	n/a	n/a
8	GATA1	chr17:46623454-46626306	PBDE	blood:	n/a	n/a
9	CUX1	chr17:46624454-46625622	K562	blood:	n/a	n/a
10	TCF7L2	chr17:46623886-46625674	HEK293	kidney:	n/a	n/a
11	TCF7L2	chr17:46623685-46625686	PANC-1	pancreas:	n/a	chr17:46623782-46623798 chr17:46623782-46623798
12	MAZ	chr17:46625142-46626078	K562	blood:	n/a	n/a
13	KAP1	chr17:46624241-46625575	U2OS	brain:	n/a	n/a
14	POLR2A	chr17:46625076-46625985	HUVEC	blood vessel:	n/a	n/a
15	JUND	chr17:46625267-46626141	K562	blood:	n/a	n/a
16	POLR2A	chr17:46620299-46626078	K562	blood:	n/a	n/a
17	POLR2A	chr17:46625146-46626294	K562	blood:	n/a	n/a
18	POLR2A	chr17:46624931-46626263	K562	blood:	n/a	n/a
19	MAFF	chr17:46625320-46625621	K562	blood:	n/a	n/a
20	EP300	chr17:46623582-46626390	K562	blood:	n/a	chr17:46623675-46623689 chr17:46625690-46625704 chr17:46624914-46624928 chr17:46624292-46624302 chr17:46624922-46624936 chr17:46625689-46625703 chr17:46624928-46624942 chr17:46623604-46623612
21	CEBPD	chr17:46625140-46625673	K562	blood:	n/a	chr17:46625255-46625266
22	POLR2A	chr17:46622500-46628313	K562	blood:	n/a	n/a
23	POLR2A	chr17:46623933-46625651	PBDE	blood:	n/a	n/a
24	MAFK	chr17:46624958-46625594	K562	blood:	n/a	n/a
25	POLR2A	chr17:46625126-46625670	K562	blood:	n/a	n/a
26	ZMIZ1	chr17:46625147-46625992	K562	blood:	n/a	n/a
27	POLR2A	chr17:46623771-46625637	K562	blood:	n/a	n/a
28	UBTF	chr17:46625118-46625546	K562	blood:	n/a	n/a
29	PML	chr17:46625132-46625923	K562	blood:	n/a	n/a
30	EP300	chr17:46625368-46625672	GM12878	blood:	n/a	n/a
31	MYC	chr17:46625332-46625963	K562	blood:	n/a	n/a
32	HEY1	chr17:46625361-46626200	K562	blood:	n/a	n/a
33	IRF1	chr17:46624090-46626016	K562	blood:	n/a	chr17:46625169-46625179 chr17:46624927-46624937 chr17:46625168-46625180 chr17:46625169-46625183 chr17:46624618-46624632 chr17:46624927-46624941 chr17:46625165-46625179 chr17:46625680-46625694 chr17:46624923-46624937
34	TBL1XR1	chr17:46623343-46626410	K562	blood:	n/a	n/a
35	TBP	chr17:46625331-46625647	K562	blood:	n/a	n/a
36	POLR2A	chr17:46625091-46625529	H1-neurons	neurons:	n/a	n/a
37	TAL1	chr17:46625252-46625942	K562	blood:	n/a	n/a
38	TCF12	chr17:46625411-46625603	H1-hESC	embryonic stem cell:	n/a	n/a
39	ZNF384	chr17:46625149-46625882	K562	blood:	n/a	n/a
40	POLR2A	chr17:46625135-46626128	K562	blood:	n/a	n/a
41	USF1	chr17:46625255-46626073	H1-hESC	embryonic stem cell:	n/a	chr17:46625758-46625769
42	PML	chr17:46625077-46625971	K562	blood:	n/a	n/a
43	IRF1	chr17:46623456-46625835	K562	blood:	n/a	chr17:46623678-46623691 chr17:46625169-46625179 chr17:46624927-46624937 chr17:46625168-46625180 chr17:46623676-46623690 chr17:46625169-46625183 chr17:46624618-46624632 chr17:46624927-46624941 chr17:46625165-46625179 chr17:46625680-46625694 chr17:46624923-46624937 chr17:46623680-46623690
44	BHLHE40	chr17:46625185-46626090	K562	blood:	n/a	n/a
45	TEAD4	chr17:46625090-46626108	K562	blood:	n/a	n/a
46	TAF7	chr17:46625338-46625851	K562	blood:	n/a	n/a
47	TEAD4	chr17:46624933-46625928	K562	blood:	n/a	n/a
48	USF1	chr17:46625281-46626047	K562	blood:	n/a	chr17:46625758-46625769
49	ZC3H11A	chr17:46625316-46625523	K562	blood:	n/a	n/a
50	USF1	chr17:46625428-46626001	H1-hESC	embryonic stem cell:	n/a	chr17:46625758-46625769

Variant related genes	Relation type
HOXB2	TF binding region
HOXB-AS3	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs2555111	0.85[CHB][hapmap]
rs9905165	0.80[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs999493	PNPO	cis	cerebellum	SCAN
rs999493	PNPO	cis	parietal	SCAN
rs999493	HOXB2	cis	Whole Blood	GTEx
rs999493	ACLY	cis	parietal	SCAN
rs999493	PYY	cis	parietal	SCAN
rs999493	NAGLU	cis	parietal	SCAN
rs999493	KLHL11	cis	cerebellum	SCAN
rs999493	KLHL11	cis	parietal	SCAN
rs999493	HOXB-AS1	cis	Whole Blood	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46618800-46625600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:46621200-46629600	Weak transcription	Gastric	stomach
3	chr17:46621600-46628000	Weak transcription	Pancreas	Pancrea
4	chr17:46621600-46634400	Weak transcription	Hela-S3	cervix
5	chr17:46621800-46627600	Weak transcription	Spleen	Spleen
6	chr17:46622000-46626200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr17:46622400-46625600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr17:46622400-46625600	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr17:46622400-46626200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr17:46622400-46626600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr17:46622600-46626200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
12	chr17:46622800-46627400	Weak transcription	Placenta	Placenta
13	chr17:46623200-46627400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr17:46623600-46625600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
15	chr17:46623600-46625600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr17:46623800-46625600	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr17:46623800-46625600	Enhancers	Colonic Mucosa	Colon
18	chr17:46623800-46625600	Flanking Active TSS	Fetal Stomach	stomach
19	chr17:46623800-46626200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr17:46623800-46630800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
21	chr17:46624000-46625600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr17:46624000-46625600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr17:46624000-46625600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr17:46624000-46625600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr17:46624000-46625800	Flanking Active TSS	HUVEC	blood vessel
26	chr17:46624000-46626200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr17:46624000-46629800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
28	chr17:46624200-46625600	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr17:46624200-46625600	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr17:46624200-46626800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr17:46624400-46625600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr17:46624400-46626600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
33	chr17:46624400-46627000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr17:46624400-46627400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr17:46624600-46625600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
36	chr17:46624600-46625600	Enhancers	GM12878-XiMat	blood
37	chr17:46624600-46626000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
38	chr17:46624600-46626200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr17:46624600-46627000	Enhancers	Primary T cells fromperipheralblood	blood
40	chr17:46624600-46631600	Weak transcription	Esophagus	oesophagus
41	chr17:46624800-46625600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
42	chr17:46624800-46625600	Flanking Active TSS	Fetal Kidney	kidney
43	chr17:46624800-46626200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr17:46624800-46626400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr17:46624800-46626800	Weak transcription	HSMMtube	muscle
46	chr17:46624800-46627400	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr17:46625000-46625600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr17:46625000-46625600	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr17:46625000-46625600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr17:46625000-46625600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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