Variant report

Variant	rs10025220
Chromosome Location	chr4:79457056-79457057
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11098224	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11098225	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11098228	0.86[CHB][hapmap]
rs11936220	0.92[CHB][hapmap]
rs11940309	0.86[CHB][hapmap]
rs12639818	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12639828	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12641956	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12648204	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13121431	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1390744	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1390746	0.82[EUR][1000 genomes]
rs1496594	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1496595	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1496596	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17003337	0.84[CHB][hapmap]
rs28391466	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28434623	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28514647	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2867445	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3749485	0.86[CHB][hapmap]
rs3811747	0.86[CHB][hapmap]
rs4610364	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4975070	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4975139	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56212709	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61284375	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6533756	0.84[EUR][1000 genomes]
rs7664814	0.82[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10025220	FRAS1	cis	Nerve Tibial	GTEx
rs10025220	GDI2	trans	cerebellum	SCAN
rs10025220	MRPL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79363800-79464200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:79385000-79467400	Weak transcription	Fetal Brain Male	brain
3	chr4:79393800-79467200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr4:79401000-79467200	Weak transcription	Psoas Muscle	Psoas
5	chr4:79410200-79461800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:79428200-79466200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr4:79428600-79459000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:79435600-79463000	Weak transcription	Fetal Heart	heart
9	chr4:79435600-79467200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr4:79440600-79465800	Weak transcription	Lung	lung
11	chr4:79440600-79467200	Weak transcription	Left Ventricle	heart
12	chr4:79442400-79465600	Weak transcription	Fetal Stomach	stomach
13	chr4:79444800-79472400	Weak transcription	Right Atrium	heart
14	chr4:79451400-79462800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:79451600-79461600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:79451800-79463400	Weak transcription	NHDF-Ad	bronchial
17	chr4:79451800-79463800	Weak transcription	NH-A	brain
18	chr4:79452000-79461600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:79453400-79464200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr4:79453400-79467200	Weak transcription	Placenta	Placenta
21	chr4:79454200-79457600	Enhancers	HMEC	breast
22	chr4:79454600-79458600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:79454600-79463800	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr4:79454800-79463600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:79455000-79463400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr4:79455200-79460400	Weak transcription	Esophagus	oesophagus
27	chr4:79455400-79463200	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:79455400-79464400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr4:79455600-79457200	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:79455600-79457200	Strong transcription	Fetal Intestine Small	intestine
31	chr4:79455600-79457200	Strong transcription	HepG2	liver
32	chr4:79455600-79457600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr4:79455600-79459000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr4:79455600-79459200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:79455600-79462600	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr4:79455600-79462800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:79456000-79457400	Strong transcription	Fetal Intestine Large	intestine
38	chr4:79456000-79461600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:79456000-79461600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr4:79456000-79464400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:79456200-79458200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr4:79456200-79463400	Weak transcription	HSMMtube	muscle
43	chr4:79456400-79464600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr4:79456400-79471200	Weak transcription	Fetal Kidney	kidney
45	chr4:79456600-79464000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:79456600-79464400	Weak transcription	Pancreas	Pancrea
47	chr4:79456800-79463600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:79456800-79464200	Weak transcription	Fetal Lung	lung
49	chr4:79456800-79464600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr4:79457000-79471200	Weak transcription	H9 Cell Line	embryonic stem cell

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