Variant report

Variant	rs572912064
Chromosome Location	chr3:49592152-49592153
allele	A/C
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	TAF1	chr3:49592117-49592560	H1-hESC	embryonic stem cell:	n/a	n/a
2	MYC	chr3:49592135-49592233	MCF10A-Er-Src	breast:	n/a	n/a
3	SIN3AK20	chr3:49592042-49592293	HepG2	liver:	n/a	n/a
4	MAX	chr3:49592080-49592393	MCF-7	breast:	n/a	n/a
5	REST	chr3:49591575-49592555	U87	brain:	n/a	n/a
6	REST	chr3:49591641-49592496	Hela-S3	cervix:	n/a	n/a
7	EP300	chr3:49591556-49592413	SK-N-SH	brain:	n/a	chr3:49592274-49592290 chr3:49591802-49591818 chr3:49591902-49591918 chr3:49591802-49591811 chr3:49591951-49591960 chr3:49591950-49591959
8	REST	chr3:49591668-49592709	HepG2	liver:	n/a	chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
9	MAX	chr3:49592045-49592399	A549	lung:	n/a	n/a
10	REST	chr3:49591593-49592485	MCF-7	breast:	n/a	n/a
11	REST	chr3:49590593-49593431	HL-60	blood:	n/a	chr3:49591201-49591211 chr3:49590761-49590779 chr3:49592639-49592653 chr3:49590764-49590777 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
12	REST	chr3:49591469-49592776	U87	brain:	n/a	chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
13	REST	chr3:49591798-49592348	GM12878	blood:	n/a	n/a
14	REST	chr3:49591481-49592787	GM12878	blood:	n/a	chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
15	CREB1	chr3:49592120-49592329	A549	lung:	n/a	n/a
16	RUNX3	chr3:49592076-49592325	GM12878	blood:	n/a	n/a
17	RCOR1	chr3:49591526-49592427	HepG2	liver:	n/a	n/a
18	MAZ	chr3:49591231-49592453	IMR90	lung:	n/a	n/a
19	MXI1	chr3:49592017-49592308	Hela-S3	cervix:	n/a	n/a
20	HMGN3	chr3:49591560-49592397	K562	blood:	n/a	n/a
21	REST	chr3:49591558-49592740	SK-N-SH	brain:	n/a	chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
22	CTCF	chr3:49592080-49592230	AG04449	skin:	n/a	n/a
23	TEAD4	chr3:49592075-49592456	A549	lung:	n/a	n/a
24	REST	chr3:49591648-49592672	H1-hESC	embryonic stem cell:	n/a	chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
25	NRF1	chr3:49591400-49592220	SK-N-SH	brain:	n/a	chr3:49591802-49591811 chr3:49591893-49591902 chr3:49591893-49591907 chr3:49591893-49591904 chr3:49591890-49591904 chr3:49591911-49591922 chr3:49591895-49591904 chr3:49591893-49591904
26	REST	chr3:49591520-49592852	PFSK-1	brain:	n/a	chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
27	REST	chr3:49591624-49592505	SK-N-SH	brain:	n/a	n/a
28	PAX5	chr3:49592070-49592214	GM12878	blood:	n/a	n/a
29	RAD21	chr3:49592063-49592206	K562	blood:	n/a	n/a
30	E2F6	chr3:49592081-49592287	K562	blood:	n/a	n/a
31	MAX	chr3:49591616-49592334	GM12878	blood:	n/a	n/a
32	MAX	chr3:49591123-49592666	HepG2	liver:	n/a	chr3:49591131-49591141
33	REST	chr3:49591580-49592761	HCT-116	colon:	n/a	chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
34	REST	chr3:49591543-49592638	U87	brain:	n/a	n/a
35	MAX	chr3:49591672-49592332	K562	blood:	n/a	n/a
36	MAX	chr3:49591763-49592522	HepG2	liver:	n/a	n/a
37	SIN3AK20	chr3:49592099-49592271	PFSK-1	brain:	n/a	n/a
38	MAX	chr3:49591409-49592453	K562	blood:	n/a	n/a
39	YY1	chr3:49592077-49592236	K562	blood:	n/a	n/a
40	REST	chr3:49591656-49592550	PANC-1	pancreas:	n/a	n/a
41	ZNF143	chr3:49591637-49592515	H1-hESC	embryonic stem cell:	n/a	chr3:49591802-49591812
42	SIN3A	chr3:49592067-49592266	GM12878	blood:	n/a	n/a
43	SMARCB1	chr3:49592052-49592444	Hela-S3	cervix:	n/a	n/a
44	E2F6	chr3:49592015-49592201	K562	blood:	n/a	n/a
45	YY1	chr3:49591534-49592359	K562	blood:	n/a	chr3:49591911-49591925 chr3:49591905-49591916 chr3:49591802-49591816 chr3:49591908-49591922 chr3:49591943-49591954 chr3:49591939-49591953 chr3:49591951-49591960 chr3:49591945-49591959 chr3:49591935-49591943 chr3:49591911-49591920 chr3:49591922-49591944 chr3:49591905-49591919
46	ZNF143	chr3:49591707-49592294	K562	blood:	n/a	chr3:49591802-49591812
47	PAX5	chr3:49591531-49592420	GM12892	blood:	n/a	chr3:49591800-49591809
48	SIN3AK20	chr3:49592074-49592305	H1-hESC	embryonic stem cell:	n/a	n/a
49	TAF1	chr3:49591396-49592256	ECC-1	luminal epithelium:	n/a	n/a
50	REST	chr3:49591563-49592704	PFSK-1	brain:	n/a	chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49590547..49592695-chr3:49709214..49711684,3	MCF-7	breast:
2	chr3:49591933..49593774-chr3:49706277..49708341,2	MCF-7	breast:

Variant related genes	Relation type
BSN-AS2	TF binding region
ENSG00000164062	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3325224	chr3:49590473-49593321	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49590800-49592400	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr3:49591000-49592200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr3:49591000-49592400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr3:49591000-49592400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:49591000-49592800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr3:49591200-49592400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:49591200-49592400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:49591200-49592400	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr3:49591200-49592400	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr3:49591200-49592400	Bivalent/Poised TSS	HepG2	liver
11	chr3:49591200-49592400	Active TSS	NHLF	lung
12	chr3:49591200-49592600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:49591200-49592600	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr3:49591200-49592600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:49591200-49592600	Active TSS	Fetal Brain Female	brain
16	chr3:49591200-49592800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
17	chr3:49591400-49592200	Active TSS	Aorta	Aorta
18	chr3:49591400-49592200	Active TSS	Pancreas	Pancrea
19	chr3:49591400-49592200	Active TSS	Small Intestine	intestine
20	chr3:49591400-49592400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:49591400-49592400	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr3:49591400-49592400	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr3:49591400-49592400	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr3:49591400-49592400	Active TSS	Brain Cingulate Gyrus	brain
25	chr3:49591400-49592400	Active TSS	Colon Smooth Muscle	Colon
26	chr3:49591400-49592400	Active TSS	Gastric	stomach
27	chr3:49591400-49592400	Active TSS	Left Ventricle	heart
28	chr3:49591400-49592400	Active TSS	Psoas Muscle	Psoas
29	chr3:49591400-49592400	Active TSS	Right Atrium	heart
30	chr3:49591400-49592400	Active TSS	Right Ventricle	heart
31	chr3:49591400-49592400	Active TSS	A549	lung
32	chr3:49591400-49592600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:49591400-49592600	Active TSS	Rectal Smooth Muscle	rectum
34	chr3:49591400-49592600	Active TSS	HSMM	muscle
35	chr3:49591400-49592800	Active TSS	H9 Cell Line	embryonic stem cell
36	chr3:49591400-49594400	Active TSS	Brain Anterior Caudate	brain
37	chr3:49591600-49592200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:49591600-49592200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:49591600-49592200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:49591600-49592200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr3:49591600-49592200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:49591600-49592200	Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr3:49591600-49592200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:49591600-49592200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:49591600-49592200	Active TSS	Liver	Liver
46	chr3:49591600-49592200	Active TSS	Brain Germinal Matrix	brain
47	chr3:49591600-49592200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr3:49591600-49592200	Active TSS	Lung	lung
49	chr3:49591600-49592200	Active TSS	Placenta Amnion	Placenta Amnion
50	chr3:49591600-49592200	Active TSS	Stomach Smooth Muscle	stomach

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