Variant report

Variant	rs491890
Chromosome Location	chr18:8088597-8088598
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10468772	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10853358	0.96[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs10853359	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11081352	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap]
rs11081354	0.96[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11081355	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11081356	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11081358	0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[EUR][1000 genomes]
rs12185338	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12956937	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12959661	0.85[EUR][1000 genomes]
rs1296003	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1296337	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1297388	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1298292	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1470323	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap]
rs1788069	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1942958	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1942959	0.95[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1942960	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2156236	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34398246	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs478396	0.91[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4798607	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs484494	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs486607	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs488952	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs490065	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs492841	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs493221	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs499764	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5000485	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs502843	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs503388	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs506248	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs507445	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs511993	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs545910	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs552448	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs561488	0.96[CEU][hapmap];0.85[CHB][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs561613	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs567523	0.96[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs575538	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs576519	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs583909	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs611022	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs615129	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs616698	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs618104	0.87[CEU][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs618466	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs619379	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs620346	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs623258	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs629391	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs630924	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs631838	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs635157	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs641089	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6417046	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs649598	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6506542	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap]
rs6506545	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6506546	0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[EUR][1000 genomes]
rs658110	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs674823	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs680016	0.96[CEU][hapmap];0.85[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs681491	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs693630	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7234055	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs8082776	0.92[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs8088354	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8089387	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs9807298	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs9807625	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.84[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	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs491890	MPPE1	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:8052600-8105200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr18:8065600-8101600	Weak transcription	Aorta	Aorta
3	chr18:8066200-8094000	Weak transcription	Hela-S3	cervix
4	chr18:8067400-8110200	Weak transcription	Right Ventricle	heart
5	chr18:8067600-8094800	Weak transcription	NHDF-Ad	bronchial
6	chr18:8068000-8092400	Weak transcription	Thymus	Thymus
7	chr18:8068000-8094800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr18:8068000-8100000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr18:8068400-8095200	Weak transcription	Lung	lung
10	chr18:8068400-8101600	Weak transcription	Fetal Stomach	stomach
11	chr18:8068400-8102400	Weak transcription	Fetal Thymus	thymus
12	chr18:8068600-8124800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr18:8069000-8102200	Weak transcription	Fetal Muscle Leg	muscle
14	chr18:8069000-8102400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr18:8069000-8102400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr18:8069400-8103400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr18:8069600-8102400	Weak transcription	Brain Anterior Caudate	brain
18	chr18:8070000-8093200	Weak transcription	Fetal Lung	lung
19	chr18:8070000-8097600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr18:8074200-8102400	Weak transcription	Psoas Muscle	Psoas
21	chr18:8079000-8092600	Weak transcription	Ovary	ovary
22	chr18:8080600-8091000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr18:8082200-8092600	Weak transcription	Gastric	stomach
24	chr18:8084400-8102800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr18:8084600-8102600	Weak transcription	NH-A	brain
26	chr18:8084600-8108000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr18:8084800-8088800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr18:8085200-8088600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr18:8085200-8091000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr18:8085200-8093800	Weak transcription	Osteobl	bone
31	chr18:8085200-8096600	Weak transcription	Fetal Heart	heart
32	chr18:8085200-8102800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr18:8085400-8088600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr18:8085400-8101800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr18:8085600-8093400	Weak transcription	HSMM	muscle
36	chr18:8085800-8088600	Weak transcription	Primary T cells from cord blood	blood
37	chr18:8085800-8088800	Strong transcription	A549	lung
38	chr18:8086200-8102400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr18:8086400-8102400	Weak transcription	Adipose Nuclei	Adipose
40	chr18:8086400-8102600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr18:8086600-8088600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr18:8086600-8091000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr18:8086800-8090800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr18:8087600-8088600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr18:8087800-8090800	Strong transcription	Left Ventricle	heart
46	chr18:8087800-8091400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr18:8088000-8088800	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr18:8088400-8088600	Enhancers	Rectal Smooth Muscle	rectum
49	chr18:8088400-8088800	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr18:8088400-8089000	Enhancers	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links