Variant report

Variant	rs557161588
Chromosome Location	chr3:49591863-49591864
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	POLR2A	chr3:49591524-49592002	HUVEC	blood vessel:	n/a	n/a
2	E2F6	chr3:49591619-49592041	K562	blood:	n/a	chr3:49591894-49591903 chr3:49591940-49591950
3	REST	chr3:49591685-49591949	PFSK-1	brain:	n/a	n/a
4	REST	chr3:49591575-49592555	U87	brain:	n/a	n/a
5	MAX	chr3:49591226-49592017	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr3:49591487-49592088	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr3:49591566-49591993	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:49591186-49592081	H1-hESC	embryonic stem cell:	n/a	n/a
9	FOXA1	chr3:49591681-49591924	T-47D	breast:	n/a	n/a
10	REST	chr3:49591641-49592496	Hela-S3	cervix:	n/a	n/a
11	TCF12	chr3:49591355-49591974	ECC-1	luminal epithelium:	n/a	chr3:49591403-49591413 chr3:49591404-49591411
12	MAX	chr3:49591293-49592008	A549	lung:	n/a	n/a
13	MAZ	chr3:49591551-49591954	HepG2	liver:	n/a	n/a
14	ELF1	chr3:49591695-49591961	K562	blood:	n/a	chr3:49591942-49591951 chr3:49591911-49591920
15	POLR2A	chr3:49591470-49591948	HepG2	liver:	n/a	n/a
16	POLR2A	chr3:49591410-49592072	H1-neurons	neurons:	n/a	n/a
17	POLR2A	chr3:49591564-49592106	HepG2	liver:	n/a	n/a
18	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
19	REST	chr3:49591668-49592709	HepG2	liver:	n/a	chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
20	E2F6	chr3:49591515-49592003	A549	lung:	n/a	chr3:49591894-49591903 chr3:49591940-49591950
21	POLR2A	chr3:49591506-49592083	HEK293	kidney:	n/a	n/a
22	MXI1	chr3:49591786-49591881	K562	blood:	n/a	n/a
23	POLR2A	chr3:49591485-49592045	K562	blood:	n/a	n/a
24	POLR2A	chr3:49591552-49591917	HUVEC	blood vessel:	n/a	n/a
25	REST	chr3:49591593-49592485	MCF-7	breast:	n/a	n/a
26	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
27	POLR2A	chr3:49591632-49591987	A549	lung:	n/a	n/a
28	REST	chr3:49591469-49592776	U87	brain:	n/a	chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
29	REST	chr3:49591798-49592348	GM12878	blood:	n/a	n/a
30	PAX5	chr3:49591524-49591870	GM12878	blood:	n/a	chr3:49591800-49591809
31	CREB1	chr3:49591316-49592050	H1-hESC	embryonic stem cell:	n/a	n/a
32	REST	chr3:49591481-49592787	GM12878	blood:	n/a	chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
33	EGR1	chr3:49591628-49591973	K562	blood:	n/a	chr3:49591800-49591809 chr3:49591894-49591903 chr3:49591876-49591889
34	TBP	chr3:49591432-49591920	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr3:49591505-49592058	MCF-7	breast:	n/a	n/a
36	RCOR1	chr3:49591802-49591921	Hela-S3	cervix:	n/a	n/a
37	RCOR1	chr3:49591526-49592427	HepG2	liver:	n/a	n/a
38	MAZ	chr3:49591231-49592453	IMR90	lung:	n/a	n/a
39	HMGN3	chr3:49591560-49592397	K562	blood:	n/a	n/a
40	REST	chr3:49591558-49592740	SK-N-SH	brain:	n/a	chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
41	MYC	chr3:49591632-49591940	K562	blood:	n/a	n/a
42	TAF1	chr3:49591734-49592068	H1-neurons	neurons:	n/a	n/a
43	REST	chr3:49591648-49592672	H1-hESC	embryonic stem cell:	n/a	chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
44	POLR2A	chr3:49591578-49591959	Gliobla	brain:	n/a	n/a
45	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
46	YY1	chr3:49591678-49592071	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
47	E2F4	chr3:49591662-49591955	MCF10A-Er-Src	breast:	n/a	chr3:49591838-49591849 chr3:49591894-49591903 chr3:49591940-49591950
48	POLR2A	chr3:49591541-49591911	K562	blood:	n/a	n/a
49	YY1	chr3:49591701-49592075	GM12891	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
50	REST	chr3:49591520-49592852	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:

Variant related genes	Relation type
BSN-AS2	TF binding region
BSN	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:123 , 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	chr3:49591200-49592000	Flanking Active TSS	Esophagus	oesophagus
7	chr3:49591200-49592400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:49591200-49592400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:49591200-49592400	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr3:49591200-49592400	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr3:49591200-49592400	Bivalent/Poised TSS	HepG2	liver
12	chr3:49591200-49592400	Active TSS	NHLF	lung
13	chr3:49591200-49592600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:49591200-49592600	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr3:49591200-49592600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:49591200-49592600	Active TSS	Fetal Brain Female	brain
17	chr3:49591200-49592800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
18	chr3:49591400-49592000	Flanking Active TSS	Spleen	Spleen
19	chr3:49591400-49592000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
20	chr3:49591400-49592200	Active TSS	Aorta	Aorta
21	chr3:49591400-49592200	Active TSS	Pancreas	Pancrea
22	chr3:49591400-49592200	Active TSS	Small Intestine	intestine
23	chr3:49591400-49592400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:49591400-49592400	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr3:49591400-49592400	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr3:49591400-49592400	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr3:49591400-49592400	Active TSS	Brain Cingulate Gyrus	brain
28	chr3:49591400-49592400	Active TSS	Colon Smooth Muscle	Colon
29	chr3:49591400-49592400	Active TSS	Gastric	stomach
30	chr3:49591400-49592400	Active TSS	Left Ventricle	heart
31	chr3:49591400-49592400	Active TSS	Psoas Muscle	Psoas
32	chr3:49591400-49592400	Active TSS	Right Atrium	heart
33	chr3:49591400-49592400	Active TSS	Right Ventricle	heart
34	chr3:49591400-49592400	Active TSS	A549	lung
35	chr3:49591400-49592600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:49591400-49592600	Active TSS	Rectal Smooth Muscle	rectum
37	chr3:49591400-49592600	Active TSS	HSMM	muscle
38	chr3:49591400-49592800	Active TSS	H9 Cell Line	embryonic stem cell
39	chr3:49591400-49594400	Active TSS	Brain Anterior Caudate	brain
40	chr3:49591600-49592000	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:49591600-49592200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:49591600-49592200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:49591600-49592200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr3:49591600-49592200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr3:49591600-49592200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:49591600-49592200	Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr3:49591600-49592200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:49591600-49592200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:49591600-49592200	Active TSS	Liver	Liver
50	chr3:49591600-49592200	Active TSS	Brain Germinal Matrix	brain

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