Variant report

Variant	rs4975076
Chromosome Location	chr4:79296137-79296138
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10033307	0.83[ASN][1000 genomes]
rs12643648	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1753085	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs345541	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs345542	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs384373	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs393285	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs454598	0.85[EUR][1000 genomes]
rs923020	0.85[ASN][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	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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4975076	FGF5	cis	parietal	SCAN
rs4975076	RCHY1	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79275400-79310600	Weak transcription	Aorta	Aorta
2	chr4:79284600-79353600	Weak transcription	Left Ventricle	heart
3	chr4:79285600-79296600	Weak transcription	Fetal Stomach	stomach
4	chr4:79288000-79318400	Weak transcription	Pancreas	Pancrea
5	chr4:79288200-79300200	Weak transcription	HSMMtube	muscle
6	chr4:79288400-79300200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:79290200-79310800	Weak transcription	Brain Anterior Caudate	brain
8	chr4:79290400-79297200	Strong transcription	HepG2	liver
9	chr4:79291200-79308400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:79291200-79314000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:79291800-79296600	Weak transcription	Fetal Intestine Small	intestine
12	chr4:79291800-79300200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:79291800-79301400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:79291800-79306400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:79291800-79307200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr4:79291800-79318200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr4:79292000-79300000	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:79292000-79300400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:79292000-79312000	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr4:79292200-79301000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:79292200-79306600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr4:79292200-79308400	Weak transcription	Fetal Lung	lung
23	chr4:79292200-79312200	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr4:79292400-79297600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:79292400-79310800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr4:79292400-79312000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:79292600-79300400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:79292600-79301200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr4:79293000-79300200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:79293000-79300400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:79293200-79299800	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr4:79293800-79297600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr4:79294000-79300800	Weak transcription	Fetal Heart	heart
34	chr4:79295000-79296200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
35	chr4:79295400-79298600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr4:79295400-79300800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr4:79295400-79301800	Weak transcription	Psoas Muscle	Psoas
38	chr4:79295600-79300200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:79295600-79300600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr4:79295600-79338800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:79295800-79296800	Weak transcription	Fetal Intestine Large	intestine
42	chr4:79295800-79297200	Weak transcription	Fetal Kidney	kidney
43	chr4:79295800-79298600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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