Variant report

Variant	rs59003764
Chromosome Location	chr12:12713900-12713901
allele	-/CACACACACACACACACACACA
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	TBP	chr12:12713627-12714716	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:12713681-12714935	HepG2	liver:	n/a	n/a
3	SMC3	chr12:12713758-12714720	Hela-S3	cervix:	n/a	n/a
4	FOXA1	chr12:12713736-12714275	HepG2	liver:	n/a	chr12:12714030-12714045 chr12:12713985-12713997
5	POLR2A	chr12:12713706-12714961	GM12878	blood:	n/a	n/a
6	BCLAF1	chr12:12713612-12714768	GM12878	blood:	n/a	chr12:12714732-12714745 chr12:12714735-12714748 chr12:12713831-12713840
7	POLR2A	chr12:12713503-12716782	HepG2	liver:	n/a	n/a
8	MYBL2	chr12:12713667-12714516	HepG2	liver:	n/a	chr12:12713758-12713771
9	POLR2A	chr12:12713801-12715363	Hela-S3	cervix:	n/a	n/a
10	RCOR1	chr12:12713765-12714479	K562	blood:	n/a	n/a
11	CTCF	chr12:12713880-12714030	AG09319	gingival:	n/a	n/a
12	CUX1	chr12:12713250-12714276	GM12878	blood:	n/a	n/a
13	SMC3	chr12:12713628-12714678	GM12878	blood:	n/a	n/a
14	ZNF217	chr12:12713730-12714174	MCF-7	breast:	n/a	n/a
15	CEBPB	chr12:12713887-12714323	HepG2	liver:	n/a	chr12:12714128-12714139
16	CEBPB	chr12:12713894-12714807	A549	lung:	n/a	chr12:12714128-12714139
17	MAZ	chr12:12713817-12714782	GM12878	blood:	n/a	n/a
18	SPI1	chr12:12713486-12714432	GM12878	blood:	n/a	chr12:12713831-12713840
19	EP300	chr12:12713682-12714659	GM12878	blood:	n/a	chr12:12714007-12714021 chr12:12714126-12714140 chr12:12713910-12713924 chr12:12713901-12713915
20	HDAC2	chr12:12713749-12714297	HepG2	liver:	n/a	chr12:12714143-12714157 chr12:12713913-12713927 chr12:12713988-12713997 chr12:12713909-12713923
21	HDAC2	chr12:12713720-12714295	HepG2	liver:	n/a	chr12:12714143-12714157 chr12:12713913-12713927 chr12:12713988-12713997 chr12:12713909-12713923
22	PML	chr12:12713634-12714946	GM12878	blood:	n/a	n/a
23	CHD1	chr12:12711450-12716107	GM12878	blood:	n/a	n/a
24	TCF12	chr12:12713817-12714249	HepG2	liver:	n/a	n/a
25	CHD1	chr12:12713235-12714685	H1-hESC	embryonic stem cell:	n/a	n/a
26	SMARCC2	chr12:12713739-12714796	Hela-S3	cervix:	n/a	n/a
27	RAD21	chr12:12713777-12714360	Hela-S3	cervix:	n/a	n/a
28	CEBPB	chr12:12713877-12714903	ECC-1	luminal epithelium:	n/a	chr12:12714128-12714139
29	POLR2A	chr12:12713421-12715350	GM12891	blood:	n/a	n/a
30	MAFF	chr12:12713850-12714169	HepG2	liver:	n/a	n/a
31	POLR2A	chr12:12713382-12716397	GM12878	blood:	n/a	n/a
32	BRCA1	chr12:12713877-12714319	HepG2	liver:	n/a	n/a
33	RUNX3	chr12:12713632-12714760	GM12878	blood:	n/a	n/a
34	POLR2A	chr12:12713620-12716156	GM18505	blood:	n/a	n/a
35	FOXA2	chr12:12713694-12714713	HepG2	liver:	n/a	chr12:12713985-12713997
36	MAX	chr12:12713746-12715418	A549	lung:	n/a	chr12:12714863-12714872 chr12:12714847-12714857
37	ELF1	chr12:12713689-12714158	MCF-7	breast:	n/a	n/a
38	BCLAF1	chr12:12713562-12715025	GM12878	blood:	n/a	chr12:12714772-12714785 chr12:12714841-12714854 chr12:12714732-12714745 chr12:12714735-12714748 chr12:12713831-12713840
39	TAF1	chr12:12713710-12715226	GM12878	blood:	n/a	n/a
40	POLR2A	chr12:12713627-12714299	PFSK-1	brain:	n/a	n/a
41	POLR2A	chr12:12713623-12714759	HepG2	liver:	n/a	n/a
42	STAT3	chr12:12713642-12714382	GM12878	blood:	n/a	n/a
43	TAF1	chr12:12713674-12713948	GM12891	blood:	n/a	n/a
44	TBL1XR1	chr12:12713696-12714294	GM12878	blood:	n/a	n/a
45	SPI1	chr12:12713591-12714351	HL-60	blood:	n/a	chr12:12713831-12713840
46	STAT5A	chr12:12713664-12714309	GM12878	blood:	n/a	n/a
47	TCF12	chr12:12713666-12714869	A549	lung:	n/a	chr12:12714518-12714525
48	CEBPB	chr12:12713452-12714491	GM12878	blood:	n/a	chr12:12714128-12714139
49	NFIC	chr12:12713601-12714723	HepG2	liver:	n/a	n/a
50	POLR2A	chr12:12713707-12714373	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:12418062..12421378-chr12:12712958..12715949,4	MCF-7	breast:
2	chr12:12713858..12718896-chr12:12719623..12723320,7	MCF-7	breast:
3	chr12:12710433..12719642-chr12:12755652..12767678,23	MCF-7	breast:
4	chr12:12712251..12716973-chr12:12867058..12873344,10	MCF-7	breast:
5	chr12:12712910..12717920-chr12:12867983..12871802,5	K562	blood:
6	chr12:12712965..12715376-chr12:12848428..12850169,2	K562	blood:
7	chr12:12713075..12717194-chr12:12718362..12721939,6	K562	blood:
8	chr12:12603843..12606415-chr12:12711459..12714793,4	MCF-7	breast:
9	chr12:12713899..12715883-chr12:12875674..12879074,4	MCF-7	breast:
10	chr12:12711165..12717532-chr12:12865354..12880919,24	MCF-7	breast:
11	chr12:12713736..12716645-chr12:14925588..14929665,3	MCF-7	breast:
12	chr12:12502650..12504579-chr12:12713839..12715957,2	MCF-7	breast:
13	chr12:12713891..12716367-chr3:161087265..161090021,2	MCF-7	breast:
14	chr12:12672853..12675163-chr12:12712393..12714277,2	K562	blood:
15	chr12:12713685..12716948-chr12:12760123..12768151,9	K562	blood:
16	chr12:12713534..12716816-chr12:12876902..12880504,5	K562	blood:
17	chr12:12713878..12715518-chr12:14922092..14923933,2	MCF-7	breast:
18	chr12:12509167..12512867-chr12:12713185..12715471,5	MCF-7	breast:
19	chr12:12673127..12675193-chr12:12712366..12713939,3	MCF-7	breast:
20	chr12:12636858..12639097-chr12:12712585..12714151,2	MCF-7	breast:

Variant related genes	Relation type
DUSP16	TF binding region
ENSG00000165714	Chromatin interaction
ENSG00000246705	Chromatin interaction
ENSG00000070018	Chromatin interaction
ENSG00000205791	Chromatin interaction
ENSG00000111269	Chromatin interaction
ENSG00000111261	Chromatin interaction
ENSG00000240424	Chromatin interaction
ENSG00000271370	Chromatin interaction
ENSG00000111276	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000197837	Chromatin interaction
ENSG00000111266	Chromatin interaction
ENSG00000183150	Chromatin interaction
ENSG00000178878	Chromatin interaction
ENSG00000255670	Chromatin interaction
ENSG00000256658	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758295	chr12:12620654-12783124	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2759880	chr12:12620654-12783124	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv898811	chr12:12655443-12928295	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv3325054	chr12:12713710-12717058	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12688200-12714400	Weak transcription	Gastric	stomach
2	chr12:12706600-12714400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:12711400-12716000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
4	chr12:12711600-12714000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr12:12711600-12714200	Weak transcription	Esophagus	oesophagus
6	chr12:12711600-12716000	Active TSS	GM12878-XiMat	blood
7	chr12:12711600-12716200	Active TSS	Liver	Liver
8	chr12:12711600-12716200	Active TSS	Duodenum Mucosa	Duodenum
9	chr12:12711600-12716200	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr12:12712000-12714200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr12:12712000-12716000	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr12:12712000-12716000	Active TSS	Fetal Intestine Large	intestine
13	chr12:12712000-12716200	Active TSS	Fetal Intestine Small	intestine
14	chr12:12712200-12716200	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr12:12712400-12714800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr12:12712600-12714000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:12712600-12714000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:12712600-12714000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:12712600-12716000	Active TSS	H1 Cell Line	embryonic stem cell
20	chr12:12712600-12716000	Active TSS	H9 Cell Line	embryonic stem cell
21	chr12:12712600-12716000	Active TSS	Colonic Mucosa	Colon
22	chr12:12712600-12716000	Active TSS	Fetal Brain Female	brain
23	chr12:12712600-12716000	Active TSS	Thymus	Thymus
24	chr12:12712600-12716000	Active TSS	K562	blood
25	chr12:12712600-12716200	Active TSS	NHLF	lung
26	chr12:12712800-12714600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:12712800-12716000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:12712800-12716000	Active TSS	Brain Anterior Caudate	brain
29	chr12:12712800-12716000	Active TSS	Fetal Stomach	stomach
30	chr12:12712800-12716200	Active TSS	Brain Cingulate Gyrus	brain
31	chr12:12712800-12716400	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr12:12712800-12716400	Active TSS	Fetal Muscle Trunk	muscle
33	chr12:12712800-12716400	Active TSS	Right Atrium	heart
34	chr12:12712800-12716800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:12713000-12714000	Flanking Active TSS	HMEC	breast
36	chr12:12713000-12716000	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr12:12713000-12716000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:12713000-12716000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:12713000-12716000	Active TSS	Fetal Muscle Leg	muscle
40	chr12:12713000-12716000	Active TSS	Stomach Smooth Muscle	stomach
41	chr12:12713000-12716200	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr12:12713000-12716200	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr12:12713000-12716200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr12:12713200-12714000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr12:12713200-12714200	Active TSS	Fetal Thymus	thymus
46	chr12:12713200-12714600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:12713200-12716000	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr12:12713200-12716200	Active TSS	Brain Hippocampus Middle	brain
49	chr12:12713200-12716400	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr12:12713200-12716600	Active TSS	Brain Angular Gyrus	brain

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