Variant report

Variant	rs4078252
Chromosome Location	chr5:112455467-112455468
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	chr5:112455253..112458185-chr5:112461323..112464102,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10037489	0.96[ASN][1000 genomes]
rs10519336	0.85[CHB][hapmap]
rs12109548	0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs13156718	0.88[CEU][hapmap]
rs13186032	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1443689	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1443693	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2165929	0.85[CHB][hapmap]
rs2900067	0.85[CHB][hapmap]
rs3922563	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs3922583	1.00[CEU][hapmap]
rs3922584	0.96[CEU][hapmap]
rs3922585	0.84[CEU][hapmap]
rs4078253	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs4078254	1.00[CEU][hapmap];0.84[TSI][hapmap]
rs4705542	0.81[CEU][hapmap]
rs4705543	0.88[CEU][hapmap]
rs4705544	1.00[CEU][hapmap]
rs4705780	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs4705782	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs4705783	0.96[CEU][hapmap];0.85[TSI][hapmap]
rs6594683	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs6594686	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6594687	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6859611	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6860460	0.86[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs6883605	0.81[CEU][hapmap]
rs7702177	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018344	chr5:112390951-112458853	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	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

Variant related diseases (count:1)

Disease	PMID	Source
Response to cytadine analogues (cytosine arabinoside)	24483146	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4078252	SRP19	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112431200-112461600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr5:112434000-112459200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:112450000-112459200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:112451000-112460600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:112451000-112478800	Weak transcription	Aorta	Aorta
6	chr5:112451800-112456200	Enhancers	Ovary	ovary
7	chr5:112452600-112455600	Enhancers	Fetal Lung	lung
8	chr5:112452600-112456800	Enhancers	Fetal Stomach	stomach
9	chr5:112452800-112456000	Enhancers	Fetal Muscle Leg	muscle
10	chr5:112452800-112456200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr5:112452800-112456200	Enhancers	Right Ventricle	heart
12	chr5:112452800-112457200	Enhancers	Left Ventricle	heart
13	chr5:112453000-112456200	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr5:112453400-112456200	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr5:112453600-112455600	Enhancers	Adipose Nuclei	Adipose
16	chr5:112453600-112457200	Enhancers	Right Atrium	heart
17	chr5:112453800-112456000	Enhancers	HSMMtube	muscle
18	chr5:112453800-112461800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:112454000-112455800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr5:112454200-112455600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:112454200-112456000	Enhancers	Psoas Muscle	Psoas
22	chr5:112454200-112456200	Enhancers	Placenta	Placenta
23	chr5:112454200-112457600	Enhancers	Liver	Liver
24	chr5:112454400-112456200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:112454400-112456200	Enhancers	Fetal Kidney	kidney
26	chr5:112454400-112456200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr5:112454600-112455600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr5:112454600-112455600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:112454600-112455600	Enhancers	HSMM	muscle
30	chr5:112454600-112455800	Enhancers	Lung	lung
31	chr5:112454600-112456000	Enhancers	Stomach Mucosa	stomach
32	chr5:112454600-112457200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:112454600-112459000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:112454600-112459400	Enhancers	NHDF-Ad	bronchial
35	chr5:112454600-112460600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr5:112454800-112455600	Enhancers	Muscle Satellite Cultured Cells	--
37	chr5:112454800-112455800	Enhancers	Osteobl	bone
38	chr5:112454800-112460400	Weak transcription	Brain Hippocampus Middle	brain
39	chr5:112454800-112460600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr5:112455000-112455600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr5:112455000-112455600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr5:112455000-112455800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr5:112455000-112455800	Enhancers	HMEC	breast
44	chr5:112455000-112456600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr5:112455000-112460000	Weak transcription	Fetal Brain Male	brain
46	chr5:112455000-112462200	Enhancers	Fetal Heart	heart
47	chr5:112455200-112455600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:112455200-112455600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr5:112455200-112456000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr5:112455200-112456000	Strong transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links