Variant report

Variant	rs563225742
Chromosome Location	chr12:48498358-48498359
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HDAC2	chr12:48498347-48498821	MCF-7	breast:	n/a	chr12:48498689-48498703
2	MAX	chr12:48498313-48498768	MCF-7	breast:	n/a	n/a
3	RELA	chr12:48498308-48500398	GM12878	blood:	n/a	chr12:48499466-48499475 chr12:48499466-48499475
4	HCFC1	chr12:48498126-48501600	Hela-S3	cervix:	n/a	n/a
5	GATA3	chr12:48498329-48498678	T-47D	breast:	n/a	n/a
6	GATA3	chr12:48498292-48498831	MCF-7	breast:	n/a	n/a
7	FOXA1	chr12:48498332-48498648	T-47D	breast:	n/a	n/a
8	POLR2A	chr12:48498219-48498732	GM12892	blood:	n/a	n/a
9	HDAC2	chr12:48498308-48498820	MCF-7	breast:	n/a	chr12:48498689-48498703
10	WRNIP1	chr12:48498305-48498641	GM12878	blood:	n/a	n/a
11	POLR2A	chr12:48498334-48501462	GM12891	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48497572..48499249-chr12:48549769..48551418,2	MCF-7	breast:
2	chr12:48492802..48495479-chr12:48497432..48499214,2	K562	blood:
3	chr12:48492914..48496557-chr12:48498180..48501677,4	MCF-7	breast:
4	chr12:48496939..48501728-chr12:48549612..48553634,6	MCF-7	breast:
5	chr12:48490196..48492740-chr12:48498056..48500665,3	MCF-7	breast:
6	chr12:48497586..48502171-chr12:48511099..48514258,8	MCF-7	breast:
7	chr12:48495831..48503326-chr12:48548997..48555180,8	K562	blood:
8	chr12:48497262..48501671-chr12:48511273..48513832,5	K562	blood:
9	chr12:48496389..48500489-chr12:48511491..48515053,4	K562	blood:

No data

Variant related genes	Relation type
PFKM	TF binding region
SENP1	TF binding region
ENSG00000152556	Chromatin interaction
ENSG00000177981	Chromatin interaction
ENSG00000258051	Chromatin interaction
ENSG00000079387	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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS 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 miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	esv3384217	chr12:48497934-48498463	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:48468600-48498400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:48476800-48498400	Weak transcription	Fetal Brain Male	brain
4	chr12:48477400-48498400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:48479400-48498400	Weak transcription	Aorta	Aorta
6	chr12:48483000-48498400	Weak transcription	HSMMtube	muscle
7	chr12:48483200-48498400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:48483200-48499200	Weak transcription	Small Intestine	intestine
9	chr12:48486200-48499000	Weak transcription	Gastric	stomach
10	chr12:48488200-48498400	Weak transcription	Brain Substantia Nigra	brain
11	chr12:48488200-48499200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:48488400-48498400	Weak transcription	Right Ventricle	heart
13	chr12:48489600-48498400	Weak transcription	Left Ventricle	heart
14	chr12:48489600-48499000	Weak transcription	Esophagus	oesophagus
15	chr12:48489800-48498400	Weak transcription	Thymus	Thymus
16	chr12:48490000-48498400	Weak transcription	Colonic Mucosa	Colon
17	chr12:48490600-48499000	Weak transcription	Ovary	ovary
18	chr12:48492000-48498400	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:48492000-48498400	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr12:48492000-48499000	Weak transcription	Placenta	Placenta
21	chr12:48492400-48498400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr12:48493600-48498400	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr12:48493600-48498600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:48493800-48498400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr12:48494200-48498400	Weak transcription	Fetal Muscle Leg	muscle
26	chr12:48496600-48498400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr12:48496600-48500400	Active TSS	GM12878-XiMat	blood
28	chr12:48497000-48498400	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr12:48497000-48498400	Enhancers	Liver	Liver
30	chr12:48497200-48498400	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr12:48497600-48498600	Enhancers	Fetal Heart	heart
32	chr12:48497600-48498600	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr12:48497800-48498400	Enhancers	Primary hematopoietic stem cells	blood
34	chr12:48498000-48498600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:48498000-48499200	Flanking Active TSS	Dnd41	blood
36	chr12:48498200-48498400	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr12:48498200-48498400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:48498200-48498400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:48498200-48498400	Enhancers	H9 Cell Line	embryonic stem cell
40	chr12:48498200-48498400	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr12:48498200-48498400	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr12:48498200-48498400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr12:48498200-48498400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:48498200-48498400	Enhancers	Primary B cells from cord blood	blood
45	chr12:48498200-48498400	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr12:48498200-48498400	Active TSS	Muscle Satellite Cultured Cells	--
47	chr12:48498200-48498400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr12:48498200-48498400	Enhancers	Brain Angular Gyrus	brain
49	chr12:48498200-48498400	Active TSS	Brain Germinal Matrix	brain
50	chr12:48498200-48498400	Enhancers	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links