Variant report

Variant	rs556453839
Chromosome Location	chr12:58149750-58149751
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	POLR2A	chr12:58149503-58149789	K562	blood:	n/a	n/a
2	MAZ	chr12:58149670-58150038	HepG2	liver:	n/a	n/a
3	CHD2	chr12:58149726-58150891	GM12878	blood:	n/a	n/a
4	SIN3AK20	chr12:58149514-58149918	HepG2	liver:	n/a	n/a
5	POLR2A	chr12:58149306-58149822	HCT-116	colon:	n/a	n/a
6	MAX	chr12:58149625-58149784	GM12878	blood:	n/a	n/a
7	ZBTB7A	chr12:58149618-58150086	HepG2	liver:	n/a	n/a
8	ZBTB7A	chr12:58148328-58150191	ECC-1	luminal epithelium:	n/a	chr12:58149222-58149231 chr12:58149015-58149023
9	SUZ12	chr12:58149341-58150830	NT2-D1	testis:	n/a	n/a
10	HNF4G	chr12:58149554-58149923	HepG2	liver:	n/a	chr12:58149845-58149858 chr12:58149846-58149858 chr12:58149846-58149858 chr12:58149845-58149858 chr12:58149845-58149859 chr12:58149845-58149858 chr12:58149843-58149861
11	MAX	chr12:58149318-58149781	K562	blood:	n/a	n/a
12	ZEB1	chr12:58149302-58150066	GM12878	blood:	n/a	chr12:58149709-58149720 chr12:58149708-58149717
13	POLR2A	chr12:58149531-58150055	HepG2	liver:	n/a	n/a
14	POLR2A	chr12:58149260-58149988	ECC-1	luminal epithelium:	n/a	n/a
15	MYBL2	chr12:58149529-58150327	HepG2	liver:	n/a	n/a
16	E2F6	chr12:58149620-58149812	K562	blood:	n/a	chr12:58149739-58149749
17	MAZ	chr12:58148241-58149884	K562	blood:	n/a	chr12:58149254-58149264
18	TAF1	chr12:58149565-58149971	HepG2	liver:	n/a	n/a
19	TCF3	chr12:58149510-58149850	GM12878	blood:	n/a	n/a
20	UBTF	chr12:58149247-58149922	K562	blood:	n/a	n/a
21	MYC	chr12:58149730-58149759	K562	blood:	n/a	n/a
22	HNF4A	chr12:58149601-58149966	HepG2	liver:	n/a	chr12:58149845-58149858 chr12:58149846-58149858 chr12:58149846-58149858 chr12:58149845-58149858 chr12:58149845-58149859 chr12:58149845-58149858 chr12:58149843-58149861
23	MXI1	chr12:58149712-58149760	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr12:58149539-58150072	HepG2	liver:	n/a	n/a
25	CCNT2	chr12:58149284-58149867	K562	blood:	n/a	chr12:58149290-58149299
26	POLR2A	chr12:58149575-58150067	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr12:58148463-58149842	GM15510	blood:	n/a	n/a
28	POLR2A	chr12:58149603-58150027	HepG2	liver:	n/a	n/a
29	ZBTB7A	chr12:58149750-58149893	HepG2	liver:	n/a	n/a
30	TCF12	chr12:58149262-58149932	ECC-1	luminal epithelium:	n/a	n/a
31	YY1	chr12:58148619-58149950	HepG2	liver:	n/a	chr12:58149247-58149258 chr12:58148739-58148750 chr12:58149290-58149299 chr12:58149012-58149026 chr12:58148887-58148897 chr12:58149072-58149081
32	SP1	chr12:58149618-58150015	HepG2	liver:	n/a	chr12:58149864-58149876 chr12:58149752-58149766 chr12:58149866-58149875 chr12:58149941-58149954 chr12:58149865-58149875
33	UBTF	chr12:58149290-58149893	K562	blood:	n/a	n/a
34	POLR2A	chr12:58149654-58149935	HepG2	liver:	n/a	n/a
35	REST	chr12:58149535-58149993	HepG2	liver:	n/a	chr12:58149694-58149707 chr12:58149680-58149693
36	POLR2A	chr12:58149592-58149779	MCF-7	breast:	n/a	n/a
37	HA-E2F1	chr12:58149527-58150127	MCF-7	breast:	n/a	chr12:58149739-58149749
38	ZBTB7A	chr12:58148811-58149931	K562	blood:	n/a	chr12:58149222-58149231 chr12:58149015-58149023
39	HEY1	chr12:58149427-58150130	HepG2	liver:	n/a	chr12:58149736-58149751
40	TAF1	chr12:58149311-58150078	HepG2	liver:	n/a	n/a
41	POLR2A	chr12:58149594-58150819	MCF10A-Er-Src	breast:	n/a	n/a
42	CEBPD	chr12:58149494-58150091	HepG2	liver:	n/a	n/a
43	MAX	chr12:58149137-58149885	K562	blood:	n/a	chr12:58149254-58149264
44	RCOR1	chr12:58149566-58149766	HepG2	liver:	n/a	n/a
45	HNF4A	chr12:58149697-58150040	HepG2	liver:	n/a	chr12:58149845-58149858 chr12:58149846-58149858 chr12:58149846-58149858 chr12:58149845-58149858 chr12:58149845-58149859 chr12:58149845-58149858 chr12:58149843-58149861
46	REST	chr12:58149322-58149833	ECC-1	luminal epithelium:	n/a	chr12:58149694-58149707 chr12:58149680-58149693
47	POLR2A	chr12:58149553-58149893	H1-neurons	neurons:	n/a	n/a
48	SPI1	chr12:58149740-58150539	GM12878	blood:	n/a	chr12:58150085-58150094 chr12:58150389-58150398 chr12:58150390-58150397
49	ZBTB7A	chr12:58148399-58150126	ECC-1	luminal epithelium:	n/a	chr12:58149222-58149231 chr12:58149015-58149023
50	ZEB1	chr12:58149546-58149775	GM12878	blood:	n/a	chr12:58149709-58149720 chr12:58149708-58149717

No.	Distal block	Cell Line	Cell type
1	chr12:58026019..58028946-chr12:58148453..58151531,3	K562	blood:
2	chr12:58146971..58149952-chr17:56735164..56736689,2	MCF-7	breast:
3	chr12:57912818..57918945-chr12:58145879..58149998,6	MCF-7	breast:
4	chr12:58148177..58150864-chr12:58195789..58197895,2	MCF-7	breast:
5	chr12:58147914..58149817-chr12:124454309..124457254,2	MCF-7	breast:
6	chr12:57915614..57917377-chr12:58148904..58151083,2	K562	blood:

Variant related genes	Relation type
CDK4	TF binding region
MARCH9	TF binding region
ENSG00000119242	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000270061	Chromatin interaction
ENSG00000135454	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000270039	Chromatin interaction
ENSG00000270095	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000179195	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv559045	chr12:58112189-58165085	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	nsv899123	chr12:58118248-58155023	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv826384	chr12:58124758-58157850	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
9	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
10	nsv826386	chr12:58135303-58150535	Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Weak transcription	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	esv3374332	chr12:58147710-58151058	Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
12	esv3347201	chr12:58148060-58150608	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	15 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	chr12:58148000-58149800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:58148200-58150000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr12:58148400-58149800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr12:58148400-58150400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:58148400-58150600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr12:58148600-58149800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
7	chr12:58148600-58149800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:58148600-58149800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr12:58148600-58149800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:58148600-58149800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:58148600-58149800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:58148600-58149800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr12:58148600-58149800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:58148600-58149800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
15	chr12:58148600-58149800	Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr12:58148600-58149800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:58148600-58149800	Active TSS	Liver	Liver
18	chr12:58148600-58149800	Active TSS	Brain Angular Gyrus	brain
19	chr12:58148600-58149800	Active TSS	Brain Cingulate Gyrus	brain
20	chr12:58148600-58149800	Active TSS	Brain Germinal Matrix	brain
21	chr12:58148600-58149800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:58148600-58149800	Active TSS	Brain Substantia Nigra	brain
23	chr12:58148600-58149800	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr12:58148600-58149800	Active TSS	Esophagus	oesophagus
25	chr12:58148600-58149800	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
26	chr12:58148600-58149800	Bivalent/Poised TSS	Fetal Stomach	stomach
27	chr12:58148600-58149800	Active TSS	Left Ventricle	heart
28	chr12:58148600-58149800	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr12:58148600-58149800	Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr12:58148600-58149800	Active TSS	Small Intestine	intestine
31	chr12:58148600-58149800	Active TSS	Thymus	Thymus
32	chr12:58148600-58149800	Active TSS	Spleen	Spleen
33	chr12:58148600-58149800	Active TSS	Hela-S3	cervix
34	chr12:58148600-58149800	Active TSS	HepG2	liver
35	chr12:58148600-58149800	Active TSS	HSMM	muscle
36	chr12:58148600-58149800	Active TSS	NH-A	brain
37	chr12:58148600-58149800	Active TSS	NHEK	skin
38	chr12:58148600-58150000	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr12:58148600-58150000	Active TSS	Aorta	Aorta
40	chr12:58148600-58150000	Weak transcription	Fetal Heart	heart
41	chr12:58148600-58150000	Active TSS	Ovary	ovary
42	chr12:58148600-58150000	Active TSS	Rectal Smooth Muscle	rectum
43	chr12:58148600-58150000	Active TSS	HSMMtube	muscle
44	chr12:58148600-58150000	Bivalent/Poised TSS	Osteobl	bone
45	chr12:58148600-58150200	Active TSS	Fetal Intestine Large	intestine
46	chr12:58148600-58150200	Active TSS	Right Atrium	heart
47	chr12:58148600-58150200	Active TSS	GM12878-XiMat	blood
48	chr12:58148600-58150600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr12:58148800-58149800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:58148800-58149800	Active TSS	Primary B cells from peripheral blood	blood

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