Variant report

Variant	rs10018235
Chromosome Location	chr4:79391392-79391393
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10001798	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10001918	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10026662	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1006079	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1027444	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1027449	0.85[GIH][hapmap]
rs11730871	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13106736	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1484331	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1484342	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1484343	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1496581	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1496582	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1496583	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1496584	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17003266	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2035511	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2054721	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2054722	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2627648	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2627649	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2627650	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2627651	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2627653	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2627654	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2627655	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2627656	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2645143	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2645144	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2645145	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2645146	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2645147	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2645148	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2645149	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28522970	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28566963	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2867068	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2867070	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2903470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34840208	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36095733	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3762844	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3899004	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4975065	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4975067	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4975076	0.88[MEX][hapmap]
rs62308116	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67201837	0.86[AMR][1000 genomes]
rs6816851	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs753751	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs753752	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7674053	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7699000	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs924149	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs949507	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs959539	0.92[EUR][1000 genomes];0.97[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10018235	G3BP2	cis	cerebellum	SCAN
rs10018235	PAQR3	cis	cerebellum	SCAN
rs10018235	PARM1	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79320000-79400200	Weak transcription	Psoas Muscle	Psoas
2	chr4:79343200-79431800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr4:79354000-79401600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:79363200-79409800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:79363400-79455200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:79363800-79464200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:79365600-79406400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr4:79366200-79408200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr4:79369400-79397800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr4:79372600-79395000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr4:79374000-79397600	Weak transcription	Fetal Lung	lung
12	chr4:79374200-79398800	Weak transcription	Esophagus	oesophagus
13	chr4:79376200-79398600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:79376200-79411600	Weak transcription	Fetal Stomach	stomach
15	chr4:79377000-79396200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr4:79378600-79455800	Weak transcription	Right Ventricle	heart
17	chr4:79378800-79395800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:79379800-79393200	Weak transcription	Brain Anterior Caudate	brain
19	chr4:79384600-79395600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr4:79384600-79396600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:79384600-79405400	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr4:79384800-79405000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:79384800-79405600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:79385000-79467400	Weak transcription	Fetal Brain Male	brain
25	chr4:79385800-79396600	Weak transcription	Pancreas	Pancrea
26	chr4:79385800-79398800	Weak transcription	Aorta	Aorta
27	chr4:79386000-79391800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr4:79387800-79396000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr4:79388200-79405000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr4:79388600-79397600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:79388800-79392000	Weak transcription	Fetal Muscle Leg	muscle
32	chr4:79389600-79393600	Strong transcription	Fetal Intestine Large	intestine
33	chr4:79389600-79393800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr4:79389600-79395000	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr4:79389800-79394200	Strong transcription	HSMMtube	muscle
36	chr4:79390800-79391400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:79391000-79391400	Strong transcription	Fetal Intestine Small	intestine
38	chr4:79391000-79392400	Strong transcription	Left Ventricle	heart
39	chr4:79391000-79392600	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr4:79391000-79392800	Strong transcription	Fetal Kidney	kidney
41	chr4:79391000-79393000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:79391000-79393200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:79391000-79393600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr4:79391000-79394200	Strong transcription	HepG2	liver
45	chr4:79391000-79405600	Weak transcription	Fetal Heart	heart
46	chr4:79391200-79391600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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