Variant report

Variant	rs116225534
Chromosome Location	chr3:118958842-118958843
allele	A/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	MTA3	chr3:118958771-118960073	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:118958207-118960535	MCF10A-Er-Src	breast:	n/a	n/a
3	REST	chr3:118958774-118960761	A549	lung:	n/a	n/a
4	MYBL2	chr3:118958795-118959377	HepG2	liver:	n/a	n/a
5	RCOR1	chr3:118958806-118959006	K562	blood:	n/a	n/a
6	MAX	chr3:118958795-118960787	A549	lung:	n/a	n/a
7	POLR2A	chr3:118958319-118959995	IMR90	lung:	n/a	n/a
8	GATA3	chr3:118958800-118960067	A549	lung:	n/a	n/a
9	MAZ	chr3:118958684-118958864	HepG2	liver:	n/a	n/a
10	GATA1	chr3:118958611-118960500	PBDE	blood:	n/a	chr3:118958675-118958692
11	CHD1	chr3:118958405-118960749	IMR90	lung:	n/a	chr3:118959806-118959816
12	POLR2A	chr3:118958614-118960088	HepG2	liver:	n/a	n/a
13	MXI1	chr3:118958090-118960205	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr3:118958262-118960665	HepG2	liver:	n/a	n/a
15	HEY1	chr3:118958808-118960004	HepG2	liver:	n/a	chr3:118959669-118959684 chr3:118959765-118959780 chr3:118959611-118959626
16	RCOR1	chr3:118958831-118960034	K562	blood:	n/a	n/a
17	REST	chr3:118958805-118960103	H1-neurons	neurons:	n/a	n/a
18	POLR2A	chr3:118958647-118959015	K562	blood:	n/a	n/a
19	ZNF384	chr3:118958700-118959157	GM12878	blood:	n/a	n/a
20	CREB1	chr3:118958811-118960115	HepG2	liver:	n/a	chr3:118959565-118959578
21	GATA2	chr3:118958577-118960072	SH-SY5Y	brain:	n/a	chr3:118958675-118958692
22	TCF12	chr3:118958651-118960732	A549	lung:	n/a	n/a
23	RAD21	chr3:118958647-118960912	SK-N-SH	brain:	n/a	chr3:118960499-118960518 chr3:118960508-118960517 chr3:118960503-118960517
24	MXI1	chr3:118958668-118960162	IMR90	lung:	n/a	n/a
25	SP1	chr3:118958784-118960163	A549	lung:	n/a	chr3:118958961-118958975 chr3:118959802-118959816 chr3:118959801-118959813
26	MBD4	chr3:118958815-118959465	HepG2	liver:	n/a	n/a
27	CHD1	chr3:118958714-118959035	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:118957609..118959509-chr3:119217273..119218823,2	MCF-7	breast:
2	chr3:118944759..118947412-chr3:118958236..118960502,3	MCF-7	breast:
3	chr3:118952753..118957545-chr3:118958102..118959880,7	K562	blood:
4	chr3:118948357..118951865-chr3:118958522..118961643,4	MCF-7	breast:
5	chr3:118863527..118866220-chr3:118958408..118962544,4	MCF-7	breast:
6	chr3:118903933..118906787-chr3:118956775..118959458,2	MCF-7	breast:
7	chr3:118948409..118952425-chr3:118955700..118962526,10	K562	blood:
8	chr3:118943120..118945710-chr3:118958108..118960423,2	K562	blood:
9	chr3:118954516..118958209-chr3:118958247..118961418,8	MCF-7	breast:

Variant related genes	Relation type
B4GALT4	TF binding region
ENSG00000114638	Chromatin interaction
ENSG00000144847	Chromatin interaction
ENSG00000121578	Chromatin interaction
ENSG00000113845	Chromatin interaction
ENSG00000240254	Chromatin interaction
ENSG00000163424	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv18354	chr3:118855337-119000251	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3405597	chr3:118958287-118960835	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118924400-118959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:118956800-118960000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:118956800-118960000	Active TSS	A549	lung
4	chr3:118957200-118959400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:118957200-118960200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr3:118957400-118959400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:118957400-118960200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:118957400-118960200	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr3:118957400-118960200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:118957400-118960200	Active TSS	NHDF-Ad	bronchial
11	chr3:118957600-118960000	Active TSS	Right Ventricle	heart
12	chr3:118957600-118960200	Active TSS	H1 Cell Line	embryonic stem cell
13	chr3:118957600-118960200	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr3:118957600-118960200	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr3:118957600-118960200	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr3:118957600-118960200	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr3:118957600-118960200	Active TSS	Right Atrium	heart
18	chr3:118957600-118960400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr3:118957800-118959800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:118957800-118959800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:118957800-118960000	Active TSS	H9 Cell Line	embryonic stem cell
22	chr3:118957800-118960000	Active TSS	HSMM	muscle
23	chr3:118957800-118960200	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr3:118958000-118959400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr3:118958000-118959400	Flanking Active TSS	Liver	Liver
26	chr3:118958000-118959800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:118958000-118959800	Active TSS	Fetal Intestine Large	intestine
28	chr3:118958000-118959800	Active TSS	HMEC	breast
29	chr3:118958000-118960000	Active TSS	Fetal Stomach	stomach
30	chr3:118958000-118960000	Active TSS	Placenta Amnion	Placenta Amnion
31	chr3:118958000-118960000	Active TSS	GM12878-XiMat	blood
32	chr3:118958000-118960200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr3:118958000-118960200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:118958200-118959000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:118958200-118959200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr3:118958200-118959200	Flanking Active TSS	Osteobl	bone
37	chr3:118958200-118959400	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr3:118958200-118959800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:118958200-118959800	Active TSS	K562	blood
40	chr3:118958200-118960000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:118958200-118960000	Active TSS	Fetal Intestine Small	intestine
42	chr3:118958200-118960000	Active TSS	Fetal Kidney	kidney
43	chr3:118958200-118960000	Active TSS	Ovary	ovary
44	chr3:118958200-118960200	Active TSS	NHLF	lung
45	chr3:118958400-118959000	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr3:118958400-118959000	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr3:118958400-118959200	Flanking Active TSS	Fetal Brain Female	brain
48	chr3:118958400-118959200	Flanking Active TSS	Thymus	Thymus
49	chr3:118958400-118959200	Flanking Active TSS	NH-A	brain
50	chr3:118958400-118959400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links