Variant report

Variant	rs534888307
Chromosome Location	chr12:64238066-64238067
allele	A/G
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	HA-E2F1	chr12:64237053-64238992	MCF-7	breast:	n/a	chr12:64237881-64237891 chr12:64237743-64237753 chr12:64237399-64237409 chr12:64237752-64237761 chr12:64237648-64237658
2	POLR2A	chr12:64237228-64239129	IMR90	lung:	n/a	n/a
3	MXI1	chr12:64236855-64239441	IMR90	lung:	n/a	n/a
4	EBF1	chr12:64237669-64238590	GM12878	blood:	n/a	chr12:64238347-64238360 chr12:64238347-64238358 chr12:64238349-64238358 chr12:64238339-64238348 chr12:64238339-64238348
5	NR3C1	chr12:64237520-64238093	A549	lung:	n/a	n/a
6	GABPA	chr12:64237290-64238104	MCF-7	breast:	n/a	chr12:64237752-64237761
7	TAF1	chr12:64237551-64238074	H1-hESC	embryonic stem cell:	n/a	n/a
8	ZBTB7A	chr12:64237235-64238600	ECC-1	luminal epithelium:	n/a	n/a
9	GABPA	chr12:64237345-64238360	H1-hESC	embryonic stem cell:	n/a	chr12:64237752-64237761
10	MAZ	chr12:64236869-64238998	IMR90	lung:	n/a	n/a
11	POLR2A	chr12:64237301-64238652	U87	brain:	n/a	n/a
12	SP1	chr12:64237062-64238101	A549	lung:	n/a	n/a
13	ZNF143	chr12:64237343-64238069	GM12878	blood:	n/a	chr12:64237799-64237817 chr12:64237678-64237688 chr12:64237881-64237891
14	SP1	chr12:64236984-64238133	A549	lung:	n/a	n/a
15	PML	chr12:64237210-64238774	MCF-7	breast:	n/a	n/a
16	TEAD4	chr12:64237377-64238134	ECC-1	luminal epithelium:	n/a	n/a
17	SMC3	chr12:64237003-64241021	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr12:64237448-64238142	MCF-7	breast:	n/a	n/a
19	CTCF	chr12:64237479-64238258	HCT-116	colon:	n/a	chr12:64237797-64237815 chr12:64237652-64237665 chr12:64237800-64237813 chr12:64237797-64237810
20	YY1	chr12:64237337-64238281	ECC-1	luminal epithelium:	n/a	chr12:64238260-64238274 chr12:64237877-64237891 chr12:64237743-64237757
21	TCF12	chr12:64237096-64239042	ECC-1	luminal epithelium:	n/a	chr12:64237807-64237817 chr12:64238884-64238891
22	RAD21	chr12:64236987-64240990	SK-N-SH	brain:	n/a	chr12:64237803-64237813 chr12:64237798-64237817 chr12:64238883-64238896 chr12:64238700-64238709 chr12:64239786-64239795 chr12:64237801-64237814 chr12:64237664-64237677
23	RAD21	chr12:64237094-64238988	A549	lung:	n/a	chr12:64237803-64237813 chr12:64237798-64237817 chr12:64238883-64238896 chr12:64238700-64238709 chr12:64237801-64237814 chr12:64237664-64237677
24	ZNF263	chr12:64237526-64238943	K562	blood:	n/a	chr12:64238449-64238470
25	EBF1	chr12:64237216-64238881	GM12878	blood:	n/a	chr12:64238347-64238360 chr12:64238347-64238358 chr12:64238349-64238358 chr12:64238339-64238348 chr12:64238339-64238348
26	RAD21	chr12:64237388-64238898	MCF-7	breast:	n/a	chr12:64237803-64237813 chr12:64237798-64237817 chr12:64238883-64238896 chr12:64238700-64238709 chr12:64237801-64237814 chr12:64237664-64237677
27	SIN3AK20	chr12:64237368-64238969	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr12:64237357-64238076	U87	brain:	n/a	n/a
29	CHD1	chr12:64237568-64238192	H1-hESC	embryonic stem cell:	n/a	chr12:64237713-64237723
30	MXI1	chr12:64237601-64238088	GM12878	blood:	n/a	n/a
31	EP300	chr12:64237247-64238085	ECC-1	luminal epithelium:	n/a	chr12:64237743-64237759 chr12:64237875-64237891 chr12:64237289-64237296 chr12:64237882-64237891
32	YY1	chr12:64237363-64238202	K562	blood:	n/a	chr12:64237877-64237891 chr12:64237743-64237757
33	MAX	chr12:64237263-64238216	MCF-7	breast:	n/a	n/a
34	POLR2A	chr12:64237203-64239025	HUVEC	blood vessel:	n/a	n/a
35	TAF1	chr12:64237463-64238934	A549	lung:	n/a	n/a
36	POLR2A	chr12:64237266-64238549	A549	lung:	n/a	n/a
37	POLR2A	chr12:64237448-64239091	H1-neurons	neurons:	n/a	n/a
38	POLR2A	chr12:64237294-64238995	HCT-116	colon:	n/a	n/a
39	NRF1	chr12:64237001-64238988	SK-N-SH	brain:	n/a	chr12:64237752-64237761
40	RAD21	chr12:64237314-64239037	H1-hESC	embryonic stem cell:	n/a	chr12:64237803-64237813 chr12:64237798-64237817 chr12:64238883-64238896 chr12:64238700-64238709 chr12:64237801-64237814 chr12:64237664-64237677
41	KAP1	chr12:64237329-64238863	HEK293	kidney:	n/a	n/a
42	TCF7L2	chr12:64237309-64238272	PANC-1	pancreas:	n/a	n/a
43	POLR2A	chr12:64237200-64238926	HepG2	liver:	n/a	n/a
44	MAX	chr12:64237479-64238208	H1-hESC	embryonic stem cell:	n/a	n/a
45	UBTF	chr12:64237403-64238271	K562	blood:	n/a	n/a
46	MYC	chr12:64237371-64238094	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr12:64237325-64238080	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr12:64237240-64240264	MCF10A-Er-Src	breast:	n/a	n/a
49	JUN	chr12:64237499-64238098	K562	blood:	n/a	n/a
50	POLR2A	chr12:64237352-64238864	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:64238043-64238093	GM12892	blood:	n/a
2	chr12:64238043-64238093	T-47D	breast:	n/a
3	chr12:64238043-64238093	Hela-S3	cervix:	n/a
4	chr12:64238043-64238093	HepG2	liver:	n/a
5	chr12:64238043-64238093	HEK293	kidney:	embryo
6	chr12:64238043-64238093	HUVEC	blood vessel:	n/a
7	chr12:64238043-64238093	AG04449	skin:	fetal
8	chr12:64238043-64238093	HMEC	breast:	n/a
9	chr12:64238043-64238093	HCF	heart:	n/a
10	chr12:64238043-64238093	GM19239	blood:	n/a
11	chr12:64238043-64238093	NT2-D1	testis:	n/a
12	chr12:64238043-64238093	GM06990	blood:	n/a
13	chr12:64238043-64238093	HL-60	blood:	n/a
14	chr12:64238043-64238093	RPTEC	kidney:	n/a
15	chr12:64238043-64238093	MCF-7	breast:	n/a
16	chr12:64238043-64238093	AoSMC	blood vessel:	n/a
17	chr12:64238043-64238093	H1-hESC	embryonic stem cell:	embryo
18	chr12:64238043-64238093	HIPEpiC	eye:	n/a
19	chr12:64238043-64238093	ECC-1	luminal epithelium:	n/a
20	chr12:64238043-64238093	AG04450	lung:	fetal
21	chr12:64238043-64238093	AG09319	gingival:	n/a
22	chr12:64238043-64238093	NH-A	brain:	n/a
23	chr12:64238043-64238093	LNCaP	prostate:	n/a
24	chr12:64238043-64238093	BE2_C	brain:	n/a
25	chr12:64238043-64238093	HRCEpiC	kidney:	n/a
26	chr12:64238043-64238093	SKMC	muscle:	n/a
27	chr12:64238043-64238093	HNPCEpiC	eye:	n/a
28	chr12:64238043-64238093	SAEC	small airway:	n/a
29	chr12:64238043-64238093	U87	brain:	n/a
30	chr12:64238043-64238093	NHBE	bronchial:	n/a
31	chr12:64238043-64238093	SK-N-SH	brain:	n/a
32	chr12:64238043-64238093	PANC-1	pancreas:	n/a
33	chr12:64238043-64238093	Hepatocyte	liver:	n/a
34	chr12:64238043-64238093	PFSK-1	brain:	n/a
35	chr12:64238043-64238093	HEEpiC	esophagus:	n/a
36	chr12:64238043-64238093	HRE	kidney:	n/a
37	chr12:64238043-64238093	GM12878	blood:	n/a
38	chr12:64238043-64238093	ovcar-3	ovarian:	n/a
39	chr12:64238043-64238093	ProgFib	skin:	n/a
40	chr12:64238043-64238093	HAEpiC	amniotic membrane:	n/a
41	chr12:64238043-64238093	NHDF-neo	bronchial:	n/a
42	chr12:64238043-64238093	SK-N-SH_RA	brain:	n/a
43	chr12:64238043-64238093	GM12891	blood:	n/a
44	chr12:64238043-64238093	K562	blood:	n/a
45	chr12:64238043-64238093	Jurkat	blood:	n/a
46	chr12:64238043-64238093	HPAEpiC	pulmonary alveolar:	n/a
47	chr12:64238043-64238093	A549	lung:	n/a
48	chr12:64238043-64238093	BJ	skin:	n/a
49	chr12:64238043-64238093	HRPEpiC	eye:	n/a
50	chr12:64238043-64238093	AG09309	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:64236758..64238491-chr12:64513269..64515825,2	MCF-7	breast:
2	chr12:64235952..64238772-chr12:64614485..64617363,3	K562	blood:
3	chr12:64237304..64239476-chr12:64424891..64426645,2	MCF-7	breast:
4	chr12:64234247..64239748-chr12:64612699..64616990,14	MCF-7	breast:
5	chr12:64233673..64240233-chr12:64613167..64618011,13	MCF-7	breast:
6	chr12:64172802..64174995-chr12:64236940..64239856,2	MCF-7	breast:

Variant related genes	Relation type
SRGAP1	TF binding region
SRGAP1	CpG island
ENSG00000118600	Chromatin interaction
ENSG00000174206	Chromatin interaction
ENSG00000255780	Chromatin interaction
ENSG00000255817	Chromatin interaction
ENSG00000243024	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046836	chr12:63392391-64377169	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	esv2759905	chr12:63901801-64252172	Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv2758312	chr12:63910416-64252172	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	esv2751110	chr12:63939733-64274680	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv832441	chr12:64063776-64252172	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv832442	chr12:64228071-64442771	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv1821934	chr12:64234926-64238128	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
8	esv1847797	chr12:64234926-64238128	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
9	esv1810729	chr12:64234926-64268005	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
10	esv3360781	chr12:64236510-64239058	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
11	esv11721	chr12:64237320-64238205	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
12	esv1797043	chr12:64237504-64256568	Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
13	esv1833454	chr12:64237504-64264837	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64236800-64238400	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr12:64236800-64238400	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr12:64236800-64238400	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr12:64236800-64238600	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr12:64236800-64238800	Active TSS	Fetal Brain Female	brain
6	chr12:64236800-64239600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:64236800-64239600	Active TSS	Brain Substantia Nigra	brain
8	chr12:64236800-64239600	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr12:64236800-64240200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:64236800-64240800	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr12:64237000-64238400	Active TSS	H1 Cell Line	embryonic stem cell
12	chr12:64237000-64238400	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr12:64237000-64238400	Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr12:64237000-64238400	Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr12:64237000-64238400	Active TSS	K562	blood
16	chr12:64237000-64238600	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr12:64237000-64238600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:64237000-64238600	Active TSS	Esophagus	oesophagus
19	chr12:64237000-64238600	Active TSS	Fetal Muscle Trunk	muscle
20	chr12:64237000-64239000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr12:64237000-64239000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:64237000-64239000	Active TSS	Rectal Smooth Muscle	rectum
23	chr12:64237000-64239200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:64237000-64239200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:64237000-64239200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:64237000-64239200	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr12:64237000-64239400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:64237000-64239400	Active TSS	Colon Smooth Muscle	Colon
29	chr12:64237000-64239400	Active TSS	Stomach Smooth Muscle	stomach
30	chr12:64237000-64239600	Active TSS	H9 Cell Line	embryonic stem cell
31	chr12:64237000-64239600	Active TSS	Brain Cingulate Gyrus	brain
32	chr12:64237000-64239600	Active TSS	Duodenum Mucosa	Duodenum
33	chr12:64237000-64239600	Active TSS	Fetal Lung	lung
34	chr12:64237000-64239600	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr12:64237000-64239600	Active TSS	Right Atrium	heart
36	chr12:64237000-64239600	Active TSS	Right Ventricle	heart
37	chr12:64237000-64239600	Active TSS	NH-A	brain
38	chr12:64237000-64239800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:64237000-64239800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:64237000-64239800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:64237000-64239800	Active TSS	Fetal Intestine Small	intestine
42	chr12:64237000-64239800	Active TSS	Left Ventricle	heart
43	chr12:64237000-64239800	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr12:64237000-64240000	Active TSS	Ovary	ovary
45	chr12:64237000-64240000	Active TSS	HMEC	breast
46	chr12:64237000-64240000	Active TSS	Osteobl	bone
47	chr12:64237000-64240200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:64237000-64240200	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr12:64237000-64240200	Active TSS	A549	lung
50	chr12:64237000-64240200	Active TSS	HSMMtube	muscle

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