Variant report

Variant	rs554408576
Chromosome Location	chr12:58118846-58118847
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:58116587-58118899	GM19193	blood:	n/a	n/a
2	POLR2A	chr12:58118708-58118863	MCF-7	breast:	n/a	n/a
3	SPI1	chr12:58118761-58119168	GM12891	blood:	n/a	chr12:58118890-58118903
4	POLR2A	chr12:58118770-58119486	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr12:58118707-58119029	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr12:58118602-58119069	GM12892	blood:	n/a	n/a
7	POLR2A	chr12:58118545-58119084	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr12:58116495-58119415	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:58116503-58119299	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:58116328-58119086	GM12878	blood:	n/a	n/a
11	POLR2A	chr12:58117045-58119241	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr12:58118792-58119024	K562	blood:	n/a	n/a
13	POLR2A	chr12:58112700-58119120	GM12891	blood:	n/a	n/a
14	SPI1	chr12:58118740-58119225	HL-60	blood:	n/a	chr12:58118890-58118903
15	POLR2A	chr12:58117124-58118952	GM12878	blood:	n/a	n/a
16	SPI1	chr12:58118819-58119090	GM12878	blood:	n/a	chr12:58118890-58118903
17	POLR2A	chr12:58118493-58118986	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr12:58114798-58119096	K562	blood:	n/a	n/a
19	POLR2A	chr12:58118645-58119033	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:58118749-58119029	GM12891	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58002964..58008004-chr12:58117447..58122099,5	MCF-7	breast:
2	chr12:58026571..58028240-chr12:58118727..58121626,2	MCF-7	breast:
3	chr12:57912267..57913858-chr12:58118505..58121411,2	MCF-7	breast:
4	chr12:57940714..57942505-chr12:58117953..58120525,2	MCF-7	breast:
5	chr12:58085694..58088995-chr12:58116929..58123534,7	MCF-7	breast:
6	chr12:57992481..57994669-chr12:58118545..58120936,2	MCF-7	breast:
7	chr12:56553083..56553874-chr12:58118705..58119506,2	NB4	blood:
8	chr12:58085407..58089363-chr12:58117669..58123604,12	MCF-7	breast:
9	chr12:57984405..57986520-chr12:58117809..58119763,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AGAP2-1	chr12:58117852-58119448	ENSG00000257499.1
2	lnc-AGAP2-1	chr12:58117852-58119448	ENSG00000257499.2

No data

Variant related genes	Relation type
ENSG00000257499	TF binding region
ENSG00000257342	TF binding region
AGAP2-AS1	TF binding region
ENSG00000208028	Chromatin interaction
ENSG00000166908	Chromatin interaction
ENSG00000240771	Chromatin interaction
ENSG00000175203	Chromatin interaction
ENSG00000135506	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000135454	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv1851618	chr12:58109302-58131947	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv826383	chr12:58118080-58123647	Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv899122	chr12:58118248-58137563	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	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

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58094400-58119600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:58106200-58120000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr12:58110000-58119800	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr12:58112200-58119600	Weak transcription	NHDF-Ad	bronchial
5	chr12:58113400-58119600	Weak transcription	Hela-S3	cervix
6	chr12:58113400-58119600	Weak transcription	HSMM	muscle
7	chr12:58113400-58119600	Weak transcription	NHEK	skin
8	chr12:58113600-58119200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:58113800-58119800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:58114000-58120600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr12:58114200-58119600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr12:58114400-58119000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr12:58114400-58119600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr12:58115000-58119200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:58115000-58119800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr12:58115000-58120800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:58115200-58119600	Weak transcription	HUVEC	blood vessel
18	chr12:58115200-58123600	Weak transcription	GM12878-XiMat	blood
19	chr12:58115400-58119000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr12:58115400-58119600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr12:58115400-58119600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr12:58115400-58119600	Weak transcription	HepG2	liver
23	chr12:58115600-58119000	Weak transcription	Primary B cells from cord blood	blood
24	chr12:58115600-58119200	Weak transcription	HMEC	breast
25	chr12:58115600-58119600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:58115600-58119600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:58115600-58119600	Weak transcription	Colonic Mucosa	Colon
28	chr12:58115600-58119800	Weak transcription	Pancreas	Pancrea
29	chr12:58115600-58124000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr12:58115800-58119200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:58115800-58119600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:58115800-58119600	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr12:58115800-58119600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:58115800-58119600	Weak transcription	Brain Anterior Caudate	brain
35	chr12:58115800-58119600	Weak transcription	Left Ventricle	heart
36	chr12:58115800-58119600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr12:58115800-58119600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr12:58115800-58119600	Weak transcription	NHLF	lung
39	chr12:58115800-58119800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:58115800-58119800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:58115800-58119800	Weak transcription	Liver	Liver
42	chr12:58115800-58119800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr12:58116000-58119200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:58116000-58119200	Weak transcription	Lung	lung
45	chr12:58116000-58119600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr12:58116000-58119600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr12:58116000-58119600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:58116000-58119600	Weak transcription	Adipose Nuclei	Adipose
49	chr12:58116000-58119600	Weak transcription	Colon Smooth Muscle	Colon
50	chr12:58116000-58119600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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