Variant report

Variant	rs572552744
Chromosome Location	chr9:2019061-2019062
allele	C/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	CEBPB	chr9:2017492-2019116	Hela-S3	cervix:	n/a	chr9:2018337-2018350 chr9:2018337-2018348
2	NANOG	chr9:2018772-2019199	H1-hESC	embryonic stem cell:	n/a	chr9:2018959-2018968 chr9:2018955-2018969
3	GTF2F1	chr9:2018980-2019147	H1-hESC	embryonic stem cell:	n/a	n/a
4	POU5F1	chr9:2018705-2019156	H1-hESC	embryonic stem cell:	n/a	chr9:2019051-2019065 chr9:2018957-2018971 chr9:2018957-2018971 chr9:2018958-2018972 chr9:2018799-2018813 chr9:2018798-2018812 chr9:2018957-2018971 chr9:2019051-2019065 chr9:2018798-2018812 chr9:2018798-2018812
5	SP1	chr9:2018678-2019305	H1-hESC	embryonic stem cell:	n/a	chr9:2019262-2019276
6	ZNF384	chr9:2019016-2019555	GM12878	blood:	n/a	n/a
7	STAT5A	chr9:2018634-2019421	GM12878	blood:	n/a	n/a
8	RUNX3	chr9:2018863-2019581	GM12878	blood:	n/a	n/a
9	EP300	chr9:2018787-2019171	H1-hESC	embryonic stem cell:	n/a	n/a
10	TCF12	chr9:2018857-2019323	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr9:2013421-2019552	GM12878	blood:	n/a	n/a
12	BCL11A	chr9:2018869-2019105	H1-hESC	embryonic stem cell:	n/a	n/a
13	HDAC2	chr9:2018729-2019253	H1-hESC	embryonic stem cell:	n/a	chr9:2019138-2019152 chr9:2019136-2019150 chr9:2019025-2019039 chr9:2019135-2019149 chr9:2019029-2019043 chr9:2019024-2019038 chr9:2019028-2019042
14	CHD1	chr9:2014303-2019408	GM12878	blood:	n/a	chr9:2016689-2016699 chr9:2015110-2015120
15	POLR2A	chr9:2014174-2019412	GM12892	blood:	n/a	n/a
16	POLR2A	chr9:2013483-2019507	GM12891	blood:	n/a	n/a
17	POLR2A	chr9:2014061-2019440	GM12878	blood:	n/a	n/a
18	SP1	chr9:2018745-2019199	H1-hESC	embryonic stem cell:	n/a	n/a
19	TCF12	chr9:2018796-2019082	H1-hESC	embryonic stem cell:	n/a	n/a
20	POU5F1	chr9:2018643-2019180	H1-hESC	embryonic stem cell:	n/a	chr9:2019051-2019065 chr9:2018957-2018971 chr9:2018957-2018971 chr9:2018958-2018972 chr9:2018799-2018813 chr9:2018798-2018812 chr9:2018957-2018971 chr9:2019051-2019065 chr9:2018798-2018812 chr9:2018798-2018812
21	WRNIP1	chr9:2017355-2019393	GM12878	blood:	n/a	n/a
22	POLR2A	chr9:2019058-2019462	GM12891	blood:	n/a	n/a
23	POLR2A	chr9:2014031-2019520	GM12878	blood:	n/a	n/a
24	MXI1	chr9:2018742-2019479	GM12878	blood:	n/a	n/a
25	POLR2A	chr9:2018670-2019549	GM12892	blood:	n/a	n/a
26	NANOG	chr9:2018820-2019249	H1-hESC	embryonic stem cell:	n/a	chr9:2018959-2018968 chr9:2018955-2018969

No.	Distal block	Cell Line	Cell type
1	chr9:2014683..2019202-chr9:2026620..2030174,6	MCF-7	breast:
2	chr9:2013479..2017608-chr9:2017826..2022083,7	MCF-7	breast:
3	chr9:2016568..2019114-chr9:2030660..2033552,2	MCF-7	breast:
4	chr9:2018308..2020609-chr9:2085608..2087272,2	K562	blood:

Variant related genes	Relation type
SMARCA2	TF binding region
ENSG00000080503	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016148	chr9:1457605-2361750	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv539916	chr9:1457605-2361750	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1021712	chr9:1647840-2216839	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv539921	chr9:1647840-2216839	Bivalent Enhancer Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv831493	chr9:1885733-2074135	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv892048	chr9:1888703-2177391	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1021158	chr9:1963930-2040728	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv892052	chr9:1980819-2072470	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	esv2830420	chr9:1998911-2119702	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv613079	chr9:2012767-2059341	Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv466069	chr9:2018825-2066493	Strong transcription Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv613080	chr9:2018825-2066493	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2014000-2019200	Active TSS	Aorta	Aorta
2	chr9:2014000-2019200	Active TSS	Ovary	ovary
3	chr9:2014000-2019600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr9:2014000-2020000	Active TSS	Right Atrium	heart
5	chr9:2014200-2019200	Active TSS	Sigmoid Colon	Sigmoid Colon
6	chr9:2014200-2021400	Active TSS	GM12878-XiMat	blood
7	chr9:2014400-2019400	Active TSS	Fetal Muscle Trunk	muscle
8	chr9:2014600-2019400	Active TSS	Placenta	Placenta
9	chr9:2016000-2019200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:2017800-2019200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
11	chr9:2017800-2019600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr9:2017800-2019800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr9:2018000-2019200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr9:2018000-2019200	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr9:2018000-2019600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
16	chr9:2018000-2019600	Flanking Active TSS	Fetal Brain Male	brain
17	chr9:2018000-2020800	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr9:2018000-2028200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr9:2018200-2019200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr9:2018200-2019200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr9:2018200-2019400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
22	chr9:2018200-2019400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr9:2018200-2019400	Flanking Active TSS	Liver	Liver
24	chr9:2018200-2019400	Flanking Active TSS	Brain Anterior Caudate	brain
25	chr9:2018200-2019400	Flanking Active TSS	Fetal Lung	lung
26	chr9:2018200-2019400	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr9:2018200-2019400	Flanking Active TSS	Hela-S3	cervix
28	chr9:2018200-2019600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr9:2018200-2019600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr9:2018200-2019600	Flanking Active TSS	Dnd41	blood
31	chr9:2018200-2019600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr9:2018200-2019800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:2018200-2020200	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr9:2018200-2023200	Weak transcription	Spleen	Spleen
35	chr9:2018200-2033400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr9:2018400-2019200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
37	chr9:2018400-2019200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr9:2018400-2019200	Flanking Active TSS	Fetal Heart	heart
39	chr9:2018400-2019400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr9:2018400-2019400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr9:2018400-2019400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr9:2018400-2019400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr9:2018400-2019400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr9:2018400-2019400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr9:2018400-2019400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:2018400-2019400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr9:2018400-2019400	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr9:2018400-2019400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr9:2018400-2019400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr9:2018400-2019400	Flanking Active TSS	Colon Smooth Muscle	Colon

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