Variant report

Variant	rs55917784
Chromosome Location	chr5:112504458-112504459
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112503765..112506074-chr5:112527852..112529518,2	MCF-7	breast:
2	chr5:112492254..112496189-chr5:112498530..112504608,6	K562	blood:

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10057729	0.89[EUR][1000 genomes]
rs11952815	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1348433	0.80[EUR][1000 genomes]
rs17135364	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7717494	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7718971	0.85[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55917784	SRP19	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112493800-112504600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr5:112495800-112506400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:112496000-112506000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:112499400-112506400	Weak transcription	Adipose Nuclei	Adipose
5	chr5:112500000-112507000	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:112500800-112506000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr5:112500800-112513800	Weak transcription	Lung	lung
8	chr5:112500800-112518400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:112501400-112504800	Weak transcription	Stomach Mucosa	stomach
10	chr5:112501400-112505200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:112501800-112506200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:112502000-112507000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:112502400-112504800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr5:112502800-112504600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr5:112503000-112504600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr5:112503000-112504600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:112503000-112504600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr5:112503000-112505000	Weak transcription	Right Atrium	heart
19	chr5:112503000-112513600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr5:112503200-112504800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr5:112503200-112504800	Weak transcription	Liver	Liver
22	chr5:112503200-112504800	Weak transcription	Fetal Heart	heart
23	chr5:112503200-112505000	Weak transcription	Placenta	Placenta
24	chr5:112503200-112505000	Weak transcription	Hela-S3	cervix
25	chr5:112503200-112505600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr5:112503200-112514000	Weak transcription	Fetal Stomach	stomach
27	chr5:112503600-112505800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:112503600-112510800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr5:112503800-112505400	Weak transcription	Fetal Lung	lung
30	chr5:112503800-112505800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:112503800-112514800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr5:112504000-112505600	Enhancers	HMEC	breast
33	chr5:112504000-112506200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr5:112504000-112507200	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr5:112504000-112507400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:112504200-112504600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr5:112504200-112504600	Bivalent Enhancer	Osteobl	bone
38	chr5:112504200-112505400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:112504200-112505600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:112504200-112506000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr5:112504200-112506200	Enhancers	NHEK	skin
42	chr5:112504200-112507600	Enhancers	Left Ventricle	heart
43	chr5:112504400-112504600	Enhancers	Fetal Muscle Leg	muscle
44	chr5:112504400-112504800	Enhancers	Esophagus	oesophagus
45	chr5:112504400-112504800	Bivalent Enhancer	NH-A	brain
46	chr5:112504400-112505400	Enhancers	Ovary	ovary
47	chr5:112504400-112505800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr5:112504400-112507800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr5:112504400-112507800	Enhancers	Right Ventricle	heart
50	chr5:112504400-112512600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links