Variant report

Variant	rs9309263
Chromosome Location	chr2:55439291-55439292
allele	C/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	POLR2A	chr2:55439148-55439361	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:55439255-55439291	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55438202..55442828-chr2:55449571..55452245,4	MCF-7	breast:
2	chr2:55437973..55440553-chr2:55504006..55505515,2	K562	blood:

Variant related genes	Relation type
CLHC1	TF binding region
ENSG00000227799	Chromatin interaction
ENSG00000162994	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs13427699	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	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
3	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

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55397200-55450000	Weak transcription	NH-A	brain
2	chr2:55402800-55450000	Weak transcription	NHDF-Ad	bronchial
3	chr2:55415400-55450000	Weak transcription	GM12878-XiMat	blood
4	chr2:55416800-55450000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:55417400-55450200	Weak transcription	Placenta	Placenta
6	chr2:55417800-55450000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:55423800-55448000	Weak transcription	HSMM	muscle
8	chr2:55424200-55450000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:55424400-55442200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:55424600-55442800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:55424600-55449800	Weak transcription	Thymus	Thymus
12	chr2:55424600-55450000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:55424600-55450200	Weak transcription	Brain Germinal Matrix	brain
14	chr2:55424600-55451200	Weak transcription	HepG2	liver
15	chr2:55424800-55450200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:55425600-55449800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr2:55427400-55450200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:55427400-55450200	Weak transcription	Aorta	Aorta
19	chr2:55427400-55450600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:55427400-55450600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:55428800-55439400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr2:55429200-55449800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:55430000-55443200	Weak transcription	Fetal Intestine Small	intestine
24	chr2:55430000-55450400	Weak transcription	Left Ventricle	heart
25	chr2:55431000-55439400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:55432000-55449800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:55432000-55451200	Weak transcription	Dnd41	blood
28	chr2:55432200-55450000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:55432600-55448800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:55432800-55450000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:55432800-55450000	Weak transcription	Fetal Stomach	stomach
32	chr2:55433000-55444600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:55433000-55448800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:55433000-55448800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:55433000-55449800	Weak transcription	Pancreas	Pancrea
36	chr2:55433000-55450200	Weak transcription	Ovary	ovary
37	chr2:55433400-55450000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:55433600-55448200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:55433600-55448600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:55437000-55441800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:55438800-55439800	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr2:55439200-55439400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr2:55439200-55439600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:55439200-55439800	Enhancers	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links