Variant report

Variant	rs564418016
Chromosome Location	chr12:123318915-123318916
allele	G/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	CTCF	chr12:123318898-123319064	Hela-S3	cervix:	n/a	n/a
2	RXRA	chr12:123318827-123319115	HepG2	liver:	n/a	n/a
3	CTCF	chr12:123318720-123318990	NHDF-neo	bronchial:	n/a	n/a
4	RFX5	chr12:123318830-123319469	Hela-S3	cervix:	n/a	n/a
5	MAX	chr12:123318862-123319768	MCF-7	breast:	n/a	n/a
6	REST	chr12:123318630-123320242	H1-neurons	neurons:	n/a	chr12:123319293-123319311 chr12:123319300-123319310 chr12:123319274-123319284
7	MXI1	chr12:123318903-123319691	Hela-S3	cervix:	n/a	n/a
8	MAFK	chr12:123318899-123319537	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr12:123318900-123319050	HBMEC	blood vessel:	n/a	n/a
10	CTCF	chr12:123318820-123318970	RPTEC	kidney:	n/a	n/a
11	MAX	chr12:123318885-123319621	A549	lung:	n/a	n/a
12	CTCF	chr12:123318900-123319050	Hela-S3	cervix:	n/a	n/a
13	USF2	chr12:123318837-123319170	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr12:123318900-123319050	RPTEC	kidney:	n/a	n/a
15	TAF1	chr12:123318840-123319746	H1-neurons	neurons:	n/a	n/a
16	CTCF	chr12:123318900-123319050	NHEK	skin:	n/a	n/a
17	CTCF	chr12:123318905-123319119	K562	blood:	n/a	n/a
18	CTCF	chr12:123318880-123319030	HRPEpiC	eye:	n/a	n/a
19	CTCF	chr12:123318880-123319030	WERI-Rb-1	eye:	n/a	n/a
20	GTF2F1	chr12:123318878-123319452	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr12:123318909-123319051	Gliobla	brain:	n/a	n/a
22	RCOR1	chr12:123318892-123319468	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr12:123318900-123319050	HPF	lung:	n/a	n/a
24	CTCF	chr12:123318860-123319010	HL-60	blood:	n/a	n/a
25	RAD21	chr12:123318887-123319109	SK-N-SH_RA	brain:	n/a	n/a
26	CTCF	chr12:123318892-123319102	HUVEC	blood vessel:	n/a	n/a
27	CEBPB	chr12:123318900-123319567	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr12:123318900-123319050	AG10803	skin:	n/a	n/a
29	TCF12	chr12:123318864-123319784	A549	lung:	n/a	n/a
30	CTCF	chr12:123318840-123318990	HA-sp	spinal cord:	n/a	n/a
31	KAP1	chr12:123318890-123319551	U2OS	brain:	n/a	n/a
32	EGR1	chr12:123318741-123319245	MCF-7	breast:	n/a	chr12:123318966-123318977 chr12:123318968-123318977 chr12:123318966-123318977 chr12:123318965-123318978 chr12:123318965-123318978 chr12:123318961-123318983 chr12:123318967-123318977 chr12:123318967-123318977 chr12:123318965-123318979
33	TCF7L2	chr12:123318905-123319443	Hela-S3	cervix:	n/a	n/a
34	CTCF	chr12:123318900-123319050	AG04449	skin:	n/a	n/a
35	MAZ	chr12:123318905-123319780	Hela-S3	cervix:	n/a	n/a
36	CTCF	chr12:123318880-123319030	HEK293	kidney:	n/a	n/a
37	SP1	chr12:123318810-123319758	A549	lung:	n/a	chr12:123319628-123319640 chr12:123319630-123319639 chr12:123319613-123319627 chr12:123319636-123319650 chr12:123319609-123319623 chr12:123319629-123319643
38	TBP	chr12:123318836-123319440	Hela-S3	cervix:	n/a	n/a
39	MAX	chr12:123318906-123319440	A549	lung:	n/a	n/a
40	CTCF	chr12:123318880-123319030	HepG2	liver:	n/a	n/a
41	CTCF	chr12:123318896-123319039	HepG2	liver:	n/a	n/a
42	CTCF	chr12:123318900-123319050	HMF	breast:	n/a	n/a
43	POLR2A	chr12:123318838-123321032	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr12:123318867-123319467	Hela-S3	cervix:	n/a	n/a
45	CTCF	chr12:123318860-123319010	HUVEC	blood vessel:	n/a	n/a
46	POLR2A	chr12:123318837-123319536	Hela-S3	cervix:	n/a	n/a
47	MXI1	chr12:123318640-123321802	SK-N-SH	brain:	n/a	n/a
48	MYC	chr12:123318878-123319028	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr12:123318900-123319050	SK-N-SH_RA	brain:	n/a	n/a
50	EGR1	chr12:123318781-123319132	H1-hESC	embryonic stem cell:	n/a	chr12:123318966-123318977 chr12:123318968-123318977 chr12:123318966-123318977 chr12:123318965-123318978 chr12:123318965-123318978 chr12:123318961-123318983 chr12:123318967-123318977 chr12:123318967-123318977 chr12:123318965-123318979

No.	Distal block	Cell Line	Cell type
1	chr12:123317720..123322313-chr12:123372173..123377754,7	MCF-7	breast:
2	chr12:123317692..123320507-chr12:123463597..123466562,3	MCF-7	breast:
3	chr12:123318894..123320705-chr12:123342894..123344549,3	MCF-7	breast:
4	chr12:123257747..123262116-chr12:123318149..123321331,4	MCF-7	breast:
5	chr12:123318760..123321217-chr12:123449684..123452450,2	K562	blood:
6	chr12:123318632..123320877-chr12:123355595..123357643,2	MCF-7	breast:
7	chr12:123237061..123238610-chr12:123318389..123320839,2	MCF-7	breast:
8	chr12:123318837..123320791-chr12:123463752..123466824,3	MCF-7	breast:
9	chr12:123318440..123320805-chr12:123633475..123636263,2	MCF-7	breast:
10	chr12:123318351..123322726-chr12:123344658..123350717,8	MCF-7	breast:

Variant related genes	Relation type
HIP1R	TF binding region
ENSG00000150967	Chromatin interaction
ENSG00000130783	Chromatin interaction
ENSG00000139726	Chromatin interaction
ENSG00000090975	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000139722	Chromatin interaction
ENSG00000256152	Chromatin interaction
ENSG00000182196	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv899574	chr12:123316566-123360151	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	esv3373177	chr12:123318824-123321872	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123310400-123319200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:123311200-123319000	Weak transcription	Aorta	Aorta
3	chr12:123313800-123319200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:123315600-123319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:123316400-123319200	Weak transcription	Gastric	stomach
6	chr12:123318400-123319000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr12:123318600-123319000	Enhancers	Stomach Mucosa	stomach
8	chr12:123318800-123319000	Enhancers	H1 Cell Line	embryonic stem cell
9	chr12:123318800-123319000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:123318800-123319000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
11	chr12:123318800-123319000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:123318800-123319000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:123318800-123319000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:123318800-123319000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr12:123318800-123319000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:123318800-123319000	Active TSS	Primary B cells from cord blood	blood
17	chr12:123318800-123319000	Enhancers	Primary T cells from cord blood	blood
18	chr12:123318800-123319000	Enhancers	Primary T cells fromperipheralblood	blood
19	chr12:123318800-123319000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:123318800-123319000	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr12:123318800-123319000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr12:123318800-123319000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr12:123318800-123319000	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr12:123318800-123319000	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr12:123318800-123319000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:123318800-123319000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:123318800-123319000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:123318800-123319000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:123318800-123319000	Active TSS	Adipose Nuclei	Adipose
30	chr12:123318800-123319000	Flanking Active TSS	Brain Anterior Caudate	brain
31	chr12:123318800-123319000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
32	chr12:123318800-123319000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:123318800-123319000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr12:123318800-123319000	Flanking Active TSS	Fetal Kidney	kidney
35	chr12:123318800-123319000	Bivalent Enhancer	Fetal Muscle Leg	muscle
36	chr12:123318800-123319000	Enhancers	Placenta	Placenta
37	chr12:123318800-123319000	Bivalent Enhancer	Fetal Stomach	stomach
38	chr12:123318800-123319000	Enhancers	Pancreas	Pancrea
39	chr12:123318800-123319000	Enhancers	Rectal Smooth Muscle	rectum
40	chr12:123318800-123319000	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr12:123318800-123319000	Flanking Active TSS	HepG2	liver
42	chr12:123318800-123319000	Enhancers	HSMM	muscle
43	chr12:123318800-123319000	Active TSS	NH-A	brain
44	chr12:123318800-123319000	Enhancers	NHEK	skin
45	chr12:123318800-123319200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr12:123318800-123319200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr12:123318800-123319200	Enhancers	Primary B cells from peripheral blood	blood
48	chr12:123318800-123319200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:123318800-123319200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr12:123318800-123319200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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