Variant report

Variant	rs11728800
Chromosome Location	chr4:15474996-15474997
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1058412	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs11722737	1.00[ASN][1000 genomes]
rs11728225	1.00[ASN][1000 genomes]
rs11737539	0.83[ASN][1000 genomes]
rs12500458	0.85[CHB][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13118306	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13131700	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16892040	0.89[ASN][1000 genomes]
rs17469704	0.83[ASN][1000 genomes]
rs1861048	0.85[CEU][hapmap]
rs2080176	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs2080177	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs2110362	0.83[ASN][1000 genomes]
rs2314588	0.83[ASN][1000 genomes]
rs2314590	0.83[ASN][1000 genomes]
rs3087622	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34465372	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4063953	0.81[EUR][1000 genomes]
rs4140933	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs4140934	0.81[EUR][1000 genomes]
rs4698112	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs4698387	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698395	0.88[CEU][hapmap];0.81[GIH][hapmap]
rs6810461	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs7675761	0.88[CEU][hapmap];0.81[GIH][hapmap]
rs9993748	0.81[EUR][1000 genomes]
rs9998686	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs9998697	0.81[EUR][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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11728800	CPEB2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15471800-15480800	Weak transcription	Pancreas	Pancrea
2	chr4:15471800-15481000	Weak transcription	Spleen	Spleen
3	chr4:15472200-15475600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr4:15472200-15475600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr4:15472200-15477800	Weak transcription	Left Ventricle	heart
6	chr4:15472200-15480600	Weak transcription	HSMM	muscle
7	chr4:15472200-15480800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:15472200-15480800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:15472200-15480800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:15472200-15480800	Weak transcription	Fetal Intestine Large	intestine
11	chr4:15472200-15480800	Weak transcription	Fetal Intestine Small	intestine
12	chr4:15472200-15480800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr4:15472200-15480800	Weak transcription	Lung	lung
14	chr4:15472600-15477800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:15472600-15480800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:15472800-15475000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:15472800-15480800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:15472800-15480800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr4:15472800-15480800	Weak transcription	NHLF	lung
20	chr4:15473000-15475200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr4:15473000-15477200	Weak transcription	Ovary	ovary
22	chr4:15473000-15477800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:15473000-15480400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr4:15473000-15480800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:15473000-15480800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr4:15473000-15480800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr4:15473000-15480800	Weak transcription	Fetal Kidney	kidney
28	chr4:15473000-15480800	Weak transcription	Psoas Muscle	Psoas
29	chr4:15473200-15477200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr4:15473200-15477400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:15473200-15477600	Weak transcription	Fetal Muscle Leg	muscle
32	chr4:15473200-15477800	Weak transcription	Adipose Nuclei	Adipose
33	chr4:15473200-15477800	Weak transcription	Aorta	Aorta
34	chr4:15473200-15480800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr4:15473200-15480800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr4:15473200-15480800	Weak transcription	Fetal Heart	heart
37	chr4:15473200-15480800	Weak transcription	Fetal Lung	lung
38	chr4:15473200-15480800	Weak transcription	Fetal Stomach	stomach
39	chr4:15473200-15480800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr4:15473800-15475800	Enhancers	Colon Smooth Muscle	Colon
41	chr4:15473800-15476000	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr4:15474000-15480800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr4:15474400-15475400	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr4:15474400-15475800	Enhancers	Stomach Smooth Muscle	stomach
45	chr4:15474400-15476000	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr4:15474400-15476000	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr4:15474600-15475200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr4:15474600-15475400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr4:15474800-15475200	Weak transcription	HSMMtube	muscle
50	chr4:15474800-15475400	Enhancers	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links