Variant report

Variant	rs33562
Chromosome Location	chr5:112307856-112307857
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112306796..112308962-chr5:112312352..112314828,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172795	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs33543	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33546	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33550	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs33553	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs33556	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs33563	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs33567	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1019756	chr5:112242315-112325943	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1028759	chr5:112300490-112358514	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs33562	DCP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112294000-112311800	Weak transcription	Right Atrium	heart
2	chr5:112298200-112311800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:112300200-112311400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:112304400-112309400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:112305600-112308600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:112305600-112309400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:112305600-112309400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:112305600-112311600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:112305600-112311600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr5:112305600-112311600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:112305600-112311600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:112305600-112311800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:112305600-112312000	Weak transcription	Hela-S3	cervix
14	chr5:112305800-112310400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:112305800-112311400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr5:112305800-112311600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr5:112305800-112311600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr5:112306000-112309000	Weak transcription	K562	blood
19	chr5:112306000-112311000	Weak transcription	HepG2	liver
20	chr5:112306000-112311400	Weak transcription	A549	lung
21	chr5:112306000-112311600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr5:112306000-112311600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr5:112306000-112311800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:112306200-112308600	Weak transcription	Placenta	Placenta
25	chr5:112307200-112311400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr5:112307200-112311600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr5:112307200-112311600	Weak transcription	Fetal Kidney	kidney
28	chr5:112307400-112311400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:112307400-112311400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr5:112307800-112311200	Weak transcription	GM12878-XiMat	blood
31	chr5:112307800-112311400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:112307800-112311600	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links