Variant report

Variant	rs149006823
Chromosome Location	chr2:55495531-55495532
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:12)
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	chr2:55495499-55496934	PFSK-1	brain:	n/a	n/a
2	MBD4	chr2:55495384-55496719	HepG2	liver:	n/a	n/a
3	MBD4	chr2:55495400-55496786	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:55495522-55497897	HepG2	liver:	n/a	n/a
5	MYC	chr2:55495397-55497273	A549	lung:	n/a	n/a
6	GABPA	chr2:55495386-55497058	A549	lung:	n/a	n/a
7	SIX5	chr2:55495524-55496790	A549	lung:	n/a	n/a
8	MYBL2	chr2:55495437-55497054	HepG2	liver:	n/a	n/a
9	BCL3	chr2:55495510-55496662	A549	lung:	n/a	chr2:55496096-55496109
10	GABPA	chr2:55495499-55496733	MCF-7	breast:	n/a	n/a
11	POLR2A	chr2:55495510-55497085	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr2:55495447-55496673	GM12892	blood:	n/a	n/a
13	POLR2A	chr2:55495518-55496801	HepG2	liver:	n/a	n/a
14	POLR2A	chr2:55495384-55496972	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr2:55495523-55496715	K562	blood:	n/a	n/a
16	POLR2A	chr2:55495508-55496702	HEK293	kidney:	n/a	n/a
17	POLR2A	chr2:55495464-55497239	GM12891	blood:	n/a	n/a
18	GABPA	chr2:55495524-55496983	A549	lung:	n/a	n/a
19	POLR2A	chr2:55495487-55496904	H1-hESC	embryonic stem cell:	n/a	n/a
20	GABPA	chr2:55495302-55497183	MCF-7	breast:	n/a	n/a
21	HEY1	chr2:55495450-55496748	HepG2	liver:	n/a	n/a
22	POLR2A	chr2:55495451-55496674	GM12878	blood:	n/a	n/a
23	POLR2A	chr2:55495407-55496791	SK-N-MC	brain:	n/a	n/a
24	MAX	chr2:55495472-55496851	HepG2	liver:	n/a	n/a
25	NFIC	chr2:55495503-55496673	HepG2	liver:	n/a	n/a
26	POLR2A	chr2:55495487-55496634	K562	blood:	n/a	n/a
27	MTA3	chr2:55495462-55496793	GM12878	blood:	n/a	n/a
28	POLR2A	chr2:55495508-55496792	GM12892	blood:	n/a	n/a
29	GATA3	chr2:55495479-55496807	A549	lung:	n/a	n/a
30	POLR2A	chr2:55495521-55496839	U87	brain:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55458256..55462359-chr2:55494864..55497801,3	K562	blood:
2	chr2:55457538..55465596-chr2:55493335..55497971,13	MCF-7	breast:
3	chr2:55274992..55277411-chr2:55494676..55497816,3	K562	blood:
4	chr2:55494928..55498059-chr2:55506695..55512310,8	K562	blood:
5	chr2:55491409..55498987-chr2:55507178..55511380,11	MCF-7	breast:
6	chr2:55458256..55461079-chr2:55494634..55496499,3	K562	blood:
7	chr2:55475194..55477770-chr2:55494963..55497132,2	MCF-7	breast:
8	chr2:55458156..55461118-chr2:55494163..55499368,6	MCF-7	breast:
9	chr12:120728776..120730953-chr2:55493561..55496361,2	MCF-7	breast:
10	chr2:55494631..55497013-chr2:55842868..55845390,2	MCF-7	breast:
11	chr2:55493189..55494879-chr2:55494974..55496543,2	MCF-7	breast:
12	chr2:55274992..55276773-chr2:55494676..55496447,2	K562	blood:

No data

Variant related genes	Relation type
MTIF2	TF binding region
ENSG00000138041	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000272606	Chromatin interaction
ENSG00000162994	Chromatin interaction
ENSG00000162997	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000143947	Chromatin interaction
ENSG00000085760	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3502708	chr2:55481350-55506212	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3502709	chr2:55481350-55506212	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv525025	chr2:55483020-55505456	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	esv1799450	chr2:55494904-55520842	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55463800-55495600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55464600-55495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:55476600-55495600	Weak transcription	Esophagus	oesophagus
4	chr2:55480400-55495600	Weak transcription	Brain Substantia Nigra	brain
5	chr2:55490600-55495600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:55491400-55495600	Weak transcription	Ovary	ovary
7	chr2:55491600-55495600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:55491600-55495600	Weak transcription	Small Intestine	intestine
9	chr2:55491800-55495600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:55491800-55495600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr2:55491800-55495600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:55491800-55495600	Weak transcription	Thymus	Thymus
13	chr2:55492000-55495600	Weak transcription	Primary B cells from cord blood	blood
14	chr2:55492000-55495600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr2:55492200-55495600	Weak transcription	Gastric	stomach
16	chr2:55492200-55495600	Weak transcription	Lung	lung
17	chr2:55492200-55495600	Weak transcription	Pancreas	Pancrea
18	chr2:55492600-55495800	Weak transcription	Spleen	Spleen
19	chr2:55493400-55495600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:55494200-55495600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:55494200-55495600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:55494200-55495600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:55494600-55495600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:55494600-55495800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:55494800-55497000	Active TSS	GM12878-XiMat	blood
26	chr2:55495000-55495600	Enhancers	Fetal Brain Male	brain
27	chr2:55495000-55495600	Flanking Active TSS	HepG2	liver
28	chr2:55495200-55495600	Enhancers	Fetal Muscle Leg	muscle
29	chr2:55495200-55495800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:55495200-55497000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:55495200-55497000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:55495200-55497200	Active TSS	Psoas Muscle	Psoas
33	chr2:55495400-55495600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr2:55495400-55495600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr2:55495400-55495600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:55495400-55495600	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr2:55495400-55495600	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr2:55495400-55495600	Active TSS	Primary T cells from cord blood	blood
39	chr2:55495400-55495600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:55495400-55495600	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr2:55495400-55495600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr2:55495400-55495600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:55495400-55495600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr2:55495400-55495600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr2:55495400-55495600	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr2:55495400-55495600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:55495400-55495600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr2:55495400-55495600	Enhancers	Brain Germinal Matrix	brain
49	chr2:55495400-55495600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr2:55495400-55495600	Active TSS	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links