Variant report

Variant	rs540060110
Chromosome Location	chr12:58148966-58148967
allele	C/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	ELF1	chr12:58148483-58149066	GM12878	blood:	n/a	chr12:58148711-58148723
2	POLR2A	chr12:58148799-58149050	ECC-1	luminal epithelium:	n/a	n/a
3	YY1	chr12:58148796-58149065	SK-N-SH_RA	brain:	n/a	chr12:58149012-58149026 chr12:58148887-58148897
4	POLR2A	chr12:58148048-58149108	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr12:58148797-58149015	HCT-116	colon:	n/a	n/a
6	MAZ	chr12:58148592-58149023	HepG2	liver:	n/a	n/a
7	YY1	chr12:58148522-58148989	HCT-116	colon:	n/a	chr12:58148739-58148750 chr12:58148887-58148897
8	ZBTB7A	chr12:58148328-58150191	ECC-1	luminal epithelium:	n/a	chr12:58149222-58149231 chr12:58149015-58149023
9	CEBPD	chr12:58148690-58149040	HepG2	liver:	n/a	n/a
10	POLR2A	chr12:58148308-58149037	SK-N-MC	brain:	n/a	n/a
11	MAZ	chr12:58148352-58149685	IMR90	lung:	n/a	chr12:58149254-58149264
12	POLR2A	chr12:58148273-58149091	Raji	blood:	n/a	n/a
13	YY1	chr12:58148694-58149062	GM12892	blood:	n/a	chr12:58148739-58148750 chr12:58149012-58149026 chr12:58148887-58148897
14	MAX	chr12:58148128-58149095	ECC-1	luminal epithelium:	n/a	n/a
15	ZEB1	chr12:58148469-58149060	GM12878	blood:	n/a	n/a
16	REST	chr12:58148027-58149365	H1-neurons	neurons:	n/a	chr12:58149045-58149055 chr12:58148029-58148038 chr12:58148716-58148729 chr12:58148719-58148732 chr12:58149019-58149032
17	MAZ	chr12:58148241-58149884	K562	blood:	n/a	chr12:58149254-58149264
18	YY1	chr12:58148433-58149073	ECC-1	luminal epithelium:	n/a	chr12:58148739-58148750 chr12:58149012-58149026 chr12:58148887-58148897
19	MAZ	chr12:58148242-58149001	Hela-S3	cervix:	n/a	n/a
20	TCF3	chr12:58148491-58149054	GM12878	blood:	n/a	chr12:58148721-58148735 chr12:58148723-58148733
21	NRF1	chr12:58147820-58148990	SK-N-SH	brain:	n/a	n/a
22	UBTF	chr12:58148566-58149032	K562	blood:	n/a	n/a
23	YY1	chr12:58148694-58149064	SK-N-SH	brain:	n/a	chr12:58148739-58148750 chr12:58149012-58149026 chr12:58148887-58148897
24	CCNT2	chr12:58148217-58149059	K562	blood:	n/a	chr12:58148712-58148721
25	POLR2A	chr12:58148463-58149842	GM15510	blood:	n/a	n/a
26	YY1	chr12:58148785-58149064	GM12878	blood:	n/a	chr12:58149012-58149026 chr12:58148887-58148897
27	POLR2A	chr12:58148813-58149046	GM12878	blood:	n/a	n/a
28	YY1	chr12:58148782-58149126	GM12891	blood:	n/a	chr12:58149012-58149026 chr12:58148887-58148897 chr12:58149072-58149081
29	YY1	chr12:58148710-58149062	SK-N-SH_RA	brain:	n/a	chr12:58148739-58148750 chr12:58149012-58149026 chr12:58148887-58148897
30	ELK1	chr12:58148890-58149007	GM12878	blood:	n/a	n/a
31	POLR2A	chr12:58148075-58149073	H1-neurons	neurons:	n/a	n/a
32	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
33	POLR2A	chr12:58148494-58148986	Hela-S3	cervix:	n/a	n/a
34	YY1	chr12:58148787-58149082	K562	blood:	n/a	chr12:58149012-58149026 chr12:58148887-58148897 chr12:58149072-58149081
35	ZBTB7A	chr12:58148811-58149931	K562	blood:	n/a	chr12:58149222-58149231 chr12:58149015-58149023
36	POLR2A	chr12:58148859-58149154	HepG2	liver:	n/a	n/a
37	YY1	chr12:58148657-58149395	K562	blood:	n/a	chr12:58149247-58149258 chr12:58148739-58148750 chr12:58149290-58149299 chr12:58149012-58149026 chr12:58148887-58148897 chr12:58149072-58149081
38	POLR2A	chr12:58148878-58149043	K562	blood:	n/a	n/a
39	YY1	chr12:58148586-58149063	ECC-1	luminal epithelium:	n/a	chr12:58148739-58148750 chr12:58149012-58149026 chr12:58148887-58148897
40	YY1	chr12:58148769-58149040	GM12878	blood:	n/a	chr12:58149012-58149026 chr12:58148887-58148897
41	HMGN3	chr12:58148526-58149086	K562	blood:	n/a	n/a
42	ZBTB7A	chr12:58148399-58150126	ECC-1	luminal epithelium:	n/a	chr12:58149222-58149231 chr12:58149015-58149023
43	CHD2	chr12:58148468-58149067	GM12878	blood:	n/a	n/a
44	MAZ	chr12:58148272-58150890	GM12878	blood:	n/a	chr12:58149254-58149264
45	POLR2A	chr12:58148827-58149039	GM12878	blood:	n/a	n/a
46	POLR2A	chr12:58148405-58149027	HCT-116	colon:	n/a	n/a

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	chr12:58146595..58149356-chr12:58175469..58178051,2	K562	blood:
6	chr12:58147914..58149817-chr12:124454309..124457254,2	MCF-7	breast:
7	chr12:57915614..57917377-chr12:58148904..58151083,2	K562	blood:

Variant related genes	Relation type
CDK4	TF binding region
MARCH9	TF binding region
ENSG00000135454	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000119242	Chromatin interaction
ENSG00000270039	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000123297	Chromatin interaction
ENSG00000179195	Chromatin interaction
ENSG00000270095	Chromatin interaction
ENSG00000270061	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:124 , 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	chr12:58148200-58149000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr12:58148200-58149200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:58148200-58149600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr12:58148200-58149600	Active TSS	Psoas Muscle	Psoas
6	chr12:58148200-58150000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr12:58148400-58149600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:58148400-58149800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr12:58148400-58150400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:58148400-58150600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr12:58148600-58149000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr12:58148600-58149000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr12:58148600-58149000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:58148600-58149200	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr12:58148600-58149400	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr12:58148600-58149400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:58148600-58149400	Active TSS	Primary hematopoietic stem cells	blood
18	chr12:58148600-58149600	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:58148600-58149600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:58148600-58149600	Active TSS	Primary B cells from cord blood	blood
21	chr12:58148600-58149600	Active TSS	Primary T cells from cord blood	blood
22	chr12:58148600-58149600	Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr12:58148600-58149600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:58148600-58149600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr12:58148600-58149600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:58148600-58149600	Active TSS	Muscle Satellite Cultured Cells	--
27	chr12:58148600-58149600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr12:58148600-58149600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:58148600-58149600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:58148600-58149600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
31	chr12:58148600-58149600	Active TSS	Brain Anterior Caudate	brain
32	chr12:58148600-58149600	Active TSS	Fetal Brain Female	brain
33	chr12:58148600-58149600	Active TSS	Stomach Smooth Muscle	stomach
34	chr12:58148600-58149600	Active TSS	A549	lung
35	chr12:58148600-58149600	Active TSS	HMEC	breast
36	chr12:58148600-58149600	Bivalent/Poised TSS	HUVEC	blood vessel
37	chr12:58148600-58149800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
38	chr12:58148600-58149800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:58148600-58149800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
40	chr12:58148600-58149800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:58148600-58149800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:58148600-58149800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:58148600-58149800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr12:58148600-58149800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr12:58148600-58149800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr12:58148600-58149800	Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr12:58148600-58149800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:58148600-58149800	Active TSS	Liver	Liver
49	chr12:58148600-58149800	Active TSS	Brain Angular Gyrus	brain
50	chr12:58148600-58149800	Active TSS	Brain Cingulate Gyrus	brain

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