Variant report

Variant	rs168282
Chromosome Location	chr4:79254058-79254059
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	chr4:79248060..79250644-chr4:79254007..79255796,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11098139	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11737491	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13103319	0.84[AMR][1000 genomes]
rs345493	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs345494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs345495	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs345496	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs345497	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs345498	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs345499	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs345500	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs345501	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs367279	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs384373	0.83[EUR][1000 genomes]
rs436034	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs454598	0.83[EUR][1000 genomes]
rs506863	0.82[AMR][1000 genomes]
rs531553	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67050216	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv525530	chr4:79024524-79266563	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1010782	chr4:79057839-79387207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv829978	chr4:79144453-79291868	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv4399	chr4:79251832-79284571	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs168282	FGF5	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79221200-79263000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr4:79229800-79257600	Weak transcription	Fetal Stomach	stomach
3	chr4:79230200-79268600	Weak transcription	Pancreas	Pancrea
4	chr4:79230600-79258000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:79231600-79260400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:79238000-79263200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:79240400-79263000	Weak transcription	Psoas Muscle	Psoas
8	chr4:79241600-79257600	Weak transcription	Left Ventricle	heart
9	chr4:79241800-79256400	Weak transcription	HepG2	liver
10	chr4:79247400-79257400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:79247400-79257600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr4:79247600-79254400	Weak transcription	Fetal Intestine Large	intestine
13	chr4:79250400-79257600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:79252400-79254200	Enhancers	H1 Cell Line	embryonic stem cell
15	chr4:79252400-79254600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr4:79252400-79254600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:79252400-79254600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:79252400-79254800	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr4:79252400-79254800	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr4:79252600-79254600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr4:79252600-79254600	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr4:79252800-79254600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:79252800-79254600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:79252800-79254600	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr4:79252800-79254800	Enhancers	Fetal Kidney	kidney
26	chr4:79252800-79255000	Enhancers	Fetal Heart	heart
27	chr4:79253200-79254200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr4:79253200-79254200	Weak transcription	Right Atrium	heart
29	chr4:79253200-79257600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr4:79253200-79257800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr4:79253400-79255000	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr4:79253400-79257600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:79253400-79257800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr4:79253400-79258600	Weak transcription	Placenta	Placenta
35	chr4:79253600-79255000	Enhancers	Fetal Intestine Small	intestine
36	chr4:79253800-79257600	Weak transcription	Fetal Lung	lung
37	chr4:79253800-79264800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:79254000-79254400	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr4:79254000-79254600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:79254000-79256400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr4:79254000-79256400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links