Variant report

Variant	rs13432266
Chromosome Location	chr2:54195753-54195754
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:54195426-54199062	MCF10A-Er-Src	breast:	n/a	n/a
2	EP300	chr2:54195657-54195766	GM12878	blood:	n/a	n/a
3	WRNIP1	chr2:54195625-54195787	GM12878	blood:	n/a	n/a
4	STAT3	chr2:54195479-54195777	GM12878	blood:	n/a	n/a
5	MYC	chr2:54195538-54195828	MCF10A-Er-Src	breast:	n/a	n/a
6	POU2F2	chr2:54195375-54195784	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:54195017-54195997	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:54195526-54196830	HepG2	liver:	n/a	n/a
9	CEBPB	chr2:54195435-54195860	Hela-S3	cervix:	n/a	n/a
10	TBP	chr2:54195364-54195861	GM12878	blood:	n/a	n/a
11	FOS	chr2:54195458-54195860	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr2:54195490-54199155	PBDE	blood:	n/a	n/a
13	RUNX3	chr2:54195330-54195758	GM12878	blood:	n/a	n/a
14	POLR2A	chr2:54194979-54195945	GM12878	blood:	n/a	n/a
15	BACH1	chr2:54195491-54195847	K562	blood:	n/a	n/a
16	FOXA2	chr2:54195632-54197176	HepG2	liver:	n/a	n/a
17	TBL1XR1	chr2:54195430-54195931	GM12878	blood:	n/a	n/a
18	STAT3	chr2:54195492-54195754	MCF10A-Er-Src	breast:	n/a	n/a
19	CHD1	chr2:54195365-54199244	IMR90	lung:	n/a	n/a
20	BHLHE40	chr2:54195411-54195771	GM12878	blood:	n/a	n/a
21	CHD1	chr2:54195634-54195782	GM12878	blood:	n/a	n/a
22	MYC	chr2:54195478-54195768	MCF10A-Er-Src	breast:	n/a	n/a
23	FOS	chr2:54195458-54195878	MCF10A-Er-Src	breast:	n/a	n/a
24	FOS	chr2:54195476-54195877	MCF10A-Er-Src	breast:	n/a	n/a
25	MXI1	chr2:54195676-54199239	SK-N-SH	brain:	n/a	n/a
26	CEBPB	chr2:54195425-54195891	K562	blood:	n/a	n/a
27	FOS	chr2:54195483-54195829	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr2:54195650-54195787	MCF10A-Er-Src	breast:	n/a	n/a
29	ATF2	chr2:54195302-54195770	GM12878	blood:	n/a	n/a
30	CREB1	chr2:54195370-54195809	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:54165576..54167252-chr2:54193257..54196468,3	K562	blood:
2	chr2:54195012..54197478-chr2:54219368..54222229,2	K562	blood:
3	chr2:54185625..54188123-chr2:54194333..54197670,3	MCF-7	breast:
4	chr2:54184275..54188127-chr2:54193177..54197889,6	K562	blood:
5	chr2:54157567..54166967-chr2:54194910..54201681,12	MCF-7	breast:
6	chr2:54176939..54180611-chr2:54194148..54196574,3	K562	blood:
7	chr2:54194885..54197429-chr2:55459526..55461126,2	MCF-7	breast:
8	chr2:54194904..54197235-chr2:54307312..54309509,2	K562	blood:

No data

Variant related genes	Relation type
ACYP2	TF binding region
ENSG00000162994	Chromatin interaction
ENSG00000241114	Chromatin interaction
ENSG00000068878	Chromatin interaction
ENSG00000143947	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10084204	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10194987	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12329248	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13400912	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13401566	1.00[AMR][1000 genomes]
rs13401851	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13405053	0.89[MKK][hapmap]
rs13409049	0.84[ASW][hapmap];0.86[LWK][hapmap]
rs13422211	1.00[LWK][hapmap]
rs13426251	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 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	chr2:54159400-54195800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:54176200-54196000	Weak transcription	Fetal Thymus	thymus
3	chr2:54176200-54196200	Weak transcription	Placenta	Placenta
4	chr2:54188800-54195800	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr2:54189800-54196400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:54190000-54196400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:54190400-54197000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:54190600-54195800	Weak transcription	Colonic Mucosa	Colon
9	chr2:54190600-54196400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:54190600-54197000	Weak transcription	Esophagus	oesophagus
11	chr2:54191800-54195800	Enhancers	Primary B cells from peripheral blood	blood
12	chr2:54192400-54196000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr2:54192600-54196400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:54192600-54197000	Weak transcription	Spleen	Spleen
15	chr2:54192800-54195800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr2:54193000-54196000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:54193600-54195800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr2:54193600-54196400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr2:54193800-54195800	Enhancers	Colon Smooth Muscle	Colon
20	chr2:54194000-54197000	Weak transcription	Gastric	stomach
21	chr2:54194000-54198800	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr2:54194200-54196600	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr2:54194400-54196200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:54194400-54196600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr2:54194400-54197000	Flanking Active TSS	Dnd41	blood
26	chr2:54194800-54196000	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr2:54194800-54196200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:54194800-54196200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:54194800-54196200	Flanking Active TSS	HUVEC	blood vessel
30	chr2:54194800-54198800	Active TSS	Osteobl	bone
31	chr2:54194800-54199400	Active TSS	HSMMtube	muscle
32	chr2:54195000-54195800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:54195000-54196400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:54195000-54196800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:54195000-54198800	Active TSS	HMEC	breast
36	chr2:54195000-54199200	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr2:54195000-54199400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:54195200-54195800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr2:54195200-54195800	Flanking Active TSS	K562	blood
40	chr2:54195200-54196000	Flanking Active TSS	HepG2	liver
41	chr2:54195200-54196200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr2:54195200-54196400	Flanking Active TSS	Liver	Liver
43	chr2:54195200-54197000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:54195200-54197400	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr2:54195200-54199200	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr2:54195200-54199400	Active TSS	HSMM	muscle
47	chr2:54195400-54195800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:54195400-54195800	Enhancers	Fetal Brain Female	brain
49	chr2:54195400-54195800	Active TSS	Rectal Smooth Muscle	rectum
50	chr2:54195400-54195800	Flanking Active TSS	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links