Variant report

Variant	rs540252524
Chromosome Location	chr12:123757733-123757734
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr12:123757617-123757795	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:123755747..123757789-chr12:123941373..123943090,2	K562	blood:
2	chr12:123755164..123758333-chr12:123868507..123873426,5	K562	blood:
3	chr12:123753451..123758032-chr12:123846651..123850459,6	MCF-7	breast:
4	chr12:123756249..123757789-chr12:123941373..123944326,2	K562	blood:
5	chr12:123756475..123758463-chr12:123849452..123851589,2	K562	blood:
6	chr12:123716353..123719935-chr12:123753594..123757800,6	K562	blood:
7	chr12:123718175..123719849-chr12:123755538..123757797,2	MCF-7	breast:
8	chr12:123749757..123758492-chr12:123844437..123851411,15	MCF-7	breast:
9	chr12:123755389..123758333-chr12:123866833..123870129,4	K562	blood:

No data

Variant related genes	Relation type
CDK2AP1	TF binding region
ENSG00000183955	Chromatin interaction
ENSG00000184209	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000130921	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats 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	70 gene(s)	inside rSNPs	diseases
3	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	esv1836043	chr12:123709409-123822503	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	esv3371786	chr12:123753799-123757997	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
6	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123756800-123758000	Enhancers	Spleen	Spleen
2	chr12:123756800-123758200	Flanking Active TSS	Brain Germinal Matrix	brain
3	chr12:123756800-123758400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:123757000-123757800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:123757200-123757800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr12:123757200-123758000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:123757200-123758000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:123757200-123758000	Enhancers	Fetal Stomach	stomach
9	chr12:123757200-123759200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:123757200-123761800	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr12:123757200-123762400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr12:123757200-123762600	Weak transcription	GM12878-XiMat	blood
13	chr12:123757200-123773800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr12:123757200-123774000	Weak transcription	K562	blood
15	chr12:123757200-123782600	Weak transcription	Right Atrium	heart
16	chr12:123757400-123757800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr12:123757400-123757800	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr12:123757400-123757800	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr12:123757400-123757800	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr12:123757400-123757800	Enhancers	A549	lung
21	chr12:123757400-123758000	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr12:123757400-123758000	Enhancers	H1 Cell Line	embryonic stem cell
23	chr12:123757400-123759200	Enhancers	Fetal Brain Male	brain
24	chr12:123757400-123762200	Weak transcription	HUVEC	blood vessel
25	chr12:123757600-123758000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:123757600-123758000	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr12:123757600-123758000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:123757600-123758000	Flanking Active TSS	Fetal Brain Female	brain
29	chr12:123757600-123758200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:123757600-123758200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:123757600-123762000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr12:123757600-123762000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:123757600-123762000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:123757600-123762000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:123757600-123762800	Weak transcription	NH-A	brain
36	chr12:123757600-123773400	Weak transcription	Fetal Muscle Leg	muscle
37	chr12:123757600-123773400	Weak transcription	Fetal Thymus	thymus
38	chr12:123757600-123773800	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links