Variant report

Variant	rs12938165
Chromosome Location	chr17:46534023-46534024
allele	A/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	USF1	chr17:46533871-46534312	ECC-1	luminal epithelium:	n/a	chr17:46534107-46534118
2	USF1	chr17:46533816-46534400	H1-hESC	embryonic stem cell:	n/a	chr17:46534107-46534118
3	USF1	chr17:46533877-46534312	A549	lung:	n/a	chr17:46534107-46534118
4	EBF1	chr17:46533976-46534169	GM12878	blood:	n/a	n/a
5	MAX	chr17:46533636-46535189	HCT-116	colon:	n/a	chr17:46534108-46534119 chr17:46534110-46534119 chr17:46534109-46534118 chr17:46534108-46534119 chr17:46534850-46534860 chr17:46534109-46534118 chr17:46534109-46534118 chr17:46534107-46534120
6	USF1	chr17:46533939-46534260	SK-N-SH_RA	brain:	n/a	chr17:46534107-46534118
7	POLR2A	chr17:46533891-46534363	HCT-116	colon:	n/a	n/a
8	MAX	chr17:46533788-46535178	HCT-116	colon:	n/a	chr17:46534108-46534119 chr17:46534110-46534119 chr17:46534109-46534118 chr17:46534108-46534119 chr17:46534850-46534860 chr17:46534109-46534118 chr17:46534109-46534118 chr17:46534107-46534120
9	USF2	chr17:46533920-46534292	H1-hESC	embryonic stem cell:	n/a	chr17:46534107-46534118
10	USF1	chr17:46533912-46534235	A549	lung:	n/a	chr17:46534107-46534118
11	USF2	chr17:46533939-46534302	GM12878	blood:	n/a	chr17:46534107-46534118
12	MAX	chr17:46533992-46534281	H1-hESC	embryonic stem cell:	n/a	chr17:46534108-46534119 chr17:46534110-46534119 chr17:46534109-46534118 chr17:46534108-46534119 chr17:46534109-46534118 chr17:46534109-46534118 chr17:46534107-46534120
13	USF1	chr17:46533948-46534222	SK-N-SH_RA	brain:	n/a	chr17:46534107-46534118
14	FOS	chr17:46534012-46534299	MCF10A-Er-Src	breast:	n/a	chr17:46534154-46534165
15	ATF3	chr17:46533999-46534197	K562	blood:	n/a	n/a
16	USF1	chr17:46533936-46534333	ECC-1	luminal epithelium:	n/a	chr17:46534107-46534118
17	USF1	chr17:46534018-46534189	GM12878	blood:	n/a	chr17:46534107-46534118
18	USF1	chr17:46533899-46534304	SK-N-SH	brain:	n/a	chr17:46534107-46534118
19	USF2	chr17:46533952-46534364	HepG2	liver:	n/a	chr17:46534107-46534118
20	USF1	chr17:46533986-46534180	HepG2	liver:	n/a	chr17:46534107-46534118
21	MAX	chr17:46533951-46534282	K562	blood:	n/a	chr17:46534108-46534119 chr17:46534110-46534119 chr17:46534109-46534118 chr17:46534108-46534119 chr17:46534109-46534118 chr17:46534109-46534118 chr17:46534107-46534120
22	USF1	chr17:46533877-46534384	K562	blood:	n/a	chr17:46534107-46534118
23	BHLHE40	chr17:46533967-46534257	K562	blood:	n/a	n/a
24	USF1	chr17:46533976-46534233	GM12878	blood:	n/a	chr17:46534107-46534118
25	CTCF	chr17:46534020-46534170	HEK293	kidney:	n/a	n/a
26	MAX	chr17:46533971-46534290	NB4	blood:	n/a	chr17:46534108-46534119 chr17:46534110-46534119 chr17:46534109-46534118 chr17:46534108-46534119 chr17:46534109-46534118 chr17:46534109-46534118 chr17:46534107-46534120
27	MAX	chr17:46533906-46534225	K562	blood:	n/a	chr17:46534108-46534119 chr17:46534110-46534119 chr17:46534109-46534118 chr17:46534108-46534119 chr17:46534109-46534118 chr17:46534109-46534118 chr17:46534107-46534120
28	POLR2A	chr17:46533899-46534310	HCT-116	colon:	n/a	n/a
29	EP300	chr17:46533990-46534203	K562	blood:	n/a	n/a
30	USF2	chr17:46533914-46534290	Hela-S3	cervix:	n/a	chr17:46534107-46534118
31	KAP1	chr17:46533972-46535073	HEK293	kidney:	n/a	n/a
32	RAD21	chr17:46533842-46535224	HCT-116	colon:	n/a	chr17:46534789-46534808
33	USF1	chr17:46533583-46535060	HCT-116	colon:	n/a	chr17:46534107-46534118
34	USF1	chr17:46533932-46534270	K562	blood:	n/a	chr17:46534107-46534118
35	GATA1	chr17:46532980-46534361	PBDE	blood:	n/a	chr17:46533324-46533332
36	SIN3A	chr17:46533951-46534931	H1-hESC	embryonic stem cell:	n/a	chr17:46534108-46534117
37	CTCF	chr17:46533980-46534130	Caco-2	colon:	n/a	n/a
38	USF1	chr17:46533963-46534222	HepG2	liver:	n/a	chr17:46534107-46534118
39	USF1	chr17:46533928-46534346	H1-hESC	embryonic stem cell:	n/a	chr17:46534107-46534118
40	JUND	chr17:46533988-46534271	K562	blood:	n/a	chr17:46534154-46534165
41	MAX	chr17:46533872-46534390	MCF-7	breast:	n/a	chr17:46534108-46534119 chr17:46534110-46534119 chr17:46534109-46534118 chr17:46534108-46534119 chr17:46534109-46534118 chr17:46534109-46534118 chr17:46534107-46534120
42	USF1	chr17:46533901-46534250	A549	lung:	n/a	chr17:46534107-46534118
43	USF1	chr17:46533736-46535068	HCT-116	colon:	n/a	chr17:46534107-46534118
44	KAP1	chr17:46533898-46534992	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46516365..46518843-chr17:46533348..46535328,2	K562	blood:
2	chr17:46533875..46534810-chr20:55548699..55549682,2	MCF-7	breast:
3	chr17:46523948..46525611-chr17:46533793..46535794,2	K562	blood:
4	chr17:46532678..46534272-chr17:46625300..46627846,2	K562	blood:
5	chr17:46529747..46531538-chr17:46533200..46534780,2	K562	blood:
6	chr17:46532737..46535111-chr17:46677941..46680284,2	K562	blood:
7	chr17:46532772..46535087-chr17:46626346..46628551,2	K562	blood:

Variant related genes	Relation type
ENSG00000264451	TF binding region
ENSG00000233101	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1022087	0.85[AFR][1000 genomes]
rs12941129	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12941208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12941352	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12941742	0.85[AFR][1000 genomes]
rs12946679	0.87[AFR][1000 genomes]
rs12947993	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12948331	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12948470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12950437	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34018531	0.91[AFR][1000 genomes]
rs34042333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34171724	0.82[AFR][1000 genomes]
rs34206844	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34238294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34287661	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34312987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34367404	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34488822	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34507526	0.85[AFR][1000 genomes]
rs34583963	0.91[AFR][1000 genomes]
rs34641642	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34736152	0.91[AFR][1000 genomes]
rs34938374	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34981051	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35048726	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35403206	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35441072	0.80[AFR][1000 genomes]
rs35457430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35460744	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35513747	0.87[AFR][1000 genomes]
rs35532660	0.87[AFR][1000 genomes]
rs35588100	0.82[AFR][1000 genomes]
rs35625427	0.91[AFR][1000 genomes]
rs36052366	0.87[AFR][1000 genomes]
rs55657194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56310092	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61037617	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71377353	0.87[AFR][1000 genomes]
rs71377358	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71377364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8080031	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46528800-46535200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr17:46529000-46535400	Enhancers	Fetal Thymus	thymus
3	chr17:46531400-46534400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr17:46531400-46534400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr17:46531600-46534200	Enhancers	Primary T cells from cord blood	blood
6	chr17:46531600-46534200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr17:46531600-46534200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr17:46531600-46534200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr17:46531600-46534400	Enhancers	Primary T cells fromperipheralblood	blood
10	chr17:46531600-46534400	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr17:46531600-46534400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr17:46531800-46534200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr17:46531800-46534200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr17:46531800-46534200	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr17:46531800-46534400	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr17:46532000-46535200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr17:46532200-46534200	Weak transcription	Primary B cells from cord blood	blood
18	chr17:46532800-46534400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr17:46533000-46534200	Weak transcription	Thymus	Thymus
20	chr17:46533000-46534400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr17:46533000-46534400	Enhancers	K562	blood
22	chr17:46533200-46534200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
23	chr17:46533200-46534200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
24	chr17:46533200-46534200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
25	chr17:46533400-46534200	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr17:46533400-46534200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
27	chr17:46533400-46534200	Enhancers	Stomach Mucosa	stomach
28	chr17:46533600-46534200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
29	chr17:46533600-46534200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
30	chr17:46533600-46534400	Enhancers	Fetal Intestine Large	intestine
31	chr17:46533600-46535000	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr17:46533800-46534400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr17:46533800-46534400	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr17:46533800-46534600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr17:46533800-46534600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr17:46533800-46534600	Bivalent Enhancer	Fetal Intestine Small	intestine
37	chr17:46533800-46534800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr17:46533800-46534800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr17:46533800-46534800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
40	chr17:46533800-46535200	Enhancers	Primary B cells from peripheral blood	blood
41	chr17:46534000-46534200	Enhancers	GM12878-XiMat	blood
42	chr17:46534000-46534400	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
43	chr17:46534000-46534400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr17:46534000-46534400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
45	chr17:46534000-46534400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr17:46534000-46534400	Bivalent Enhancer	HepG2	liver
47	chr17:46534000-46534400	Enhancers	NHEK	skin
48	chr17:46534000-46534600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
49	chr17:46534000-46534600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
50	chr17:46534000-46534600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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