Variant report

Variant	rs10798005
Chromosome Location	chr1:172382965-172382966
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1063412	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10752946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10752957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10798026	0.87[ASW][hapmap]
rs10911786	0.87[ASW][hapmap]
rs11484605	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12076560	0.84[ASN][1000 genomes]
rs13932	1.00[CHB][hapmap];0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs2269613	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs2269614	0.95[CHB][hapmap]
rs2269615	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs2269616	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2285170	0.95[CHB][hapmap]
rs2285171	0.95[CHB][hapmap];0.84[CHD][hapmap]
rs2285173	0.95[CHB][hapmap];0.84[CHD][hapmap]
rs2285174	0.95[CHB][hapmap]
rs2285175	0.95[CHB][hapmap]
rs2285176	0.95[CHB][hapmap]
rs2301455	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs2422141	0.95[ASN][1000 genomes]
rs3213563	0.82[ASN][1000 genomes]
rs3937046	1.00[CHB][hapmap];0.84[CHD][hapmap];0.80[ASN][1000 genomes]
rs4916186	0.98[ASN][1000 genomes]
rs4916258	0.82[ASN][1000 genomes]
rs6424923	0.95[CHB][hapmap]
rs6658843	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6673869	0.95[CHB][hapmap];0.84[CHD][hapmap]
rs6674073	0.95[CHB][hapmap]
rs6702667	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7411767	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7516301	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7528296	0.87[ASW][hapmap]
rs9425308	0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9425311	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9425313	0.95[ASN][1000 genomes]
rs9425316	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9425598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9425600	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9425601	0.97[ASN][1000 genomes]
rs9425602	0.99[ASN][1000 genomes]
rs9425604	0.99[ASN][1000 genomes]
rs9425606	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10798005	C1orf105	cis	cerebellum	SCAN
rs10798005	SNORD79	cis	cerebellum	SCAN
rs10798005	SNORD47	cis	cerebellum	SCAN
rs10798005	PIGC	cis	Whole Blood	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172352400-172386400	Weak transcription	Psoas Muscle	Psoas
2	chr1:172368400-172390800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:172370200-172385600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:172373000-172390800	Weak transcription	Brain Hippocampus Middle	brain
5	chr1:172373000-172390800	Weak transcription	Brain Substantia Nigra	brain
6	chr1:172373000-172411800	Weak transcription	Brain Angular Gyrus	brain
7	chr1:172375400-172383600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:172377200-172384400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:172378400-172385200	Weak transcription	Fetal Kidney	kidney
10	chr1:172379400-172383600	Weak transcription	NHDF-Ad	bronchial
11	chr1:172379400-172386600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:172379600-172383200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:172381200-172383000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:172381400-172383600	Weak transcription	GM12878-XiMat	blood
15	chr1:172381800-172383000	Weak transcription	NHEK	skin
16	chr1:172382200-172390800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:172382800-172383400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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