Variant report

Variant	rs10494743
Chromosome Location	chr1:196425133-196425134
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10737670	0.89[JPT][hapmap]
rs10754187	0.89[JPT][hapmap]
rs10754188	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10754195	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs10754196	0.84[JPT][hapmap]
rs10801530	0.89[JPT][hapmap]
rs10801531	0.89[JPT][hapmap]
rs10801532	0.89[JPT][hapmap]
rs10801533	0.92[CEU][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs10801537	0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs10801538	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10801539	0.93[ASN][1000 genomes]
rs10922067	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10922068	0.89[EUR][1000 genomes]
rs10922071	0.86[CHB][hapmap];0.89[CHD][hapmap];0.90[ASN][1000 genomes]
rs10922073	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10922075	0.80[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs10922082	0.94[JPT][hapmap]
rs10922083	0.94[JPT][hapmap]
rs10922084	0.94[JPT][hapmap]
rs10922088	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs11576790	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11807331	0.82[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs12034150	0.91[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs12049567	0.84[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12065463	0.83[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs12065519	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12069983	0.89[JPT][hapmap]
rs12069990	0.89[JPT][hapmap]
rs12121250	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12562176	0.89[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12727032	0.92[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap]
rs12729649	0.89[JPT][hapmap]
rs1416962	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1538684	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1538686	0.98[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1538687	0.89[JPT][hapmap]
rs16840224	0.84[JPT][hapmap]
rs1769996	0.89[JPT][hapmap]
rs1832617	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2027368	0.89[JPT][hapmap]
rs2878551	0.84[CHD][hapmap]
rs2878557	0.89[JPT][hapmap]
rs2878559	0.92[CEU][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes]
rs35582782	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3855964	0.89[JPT][hapmap]
rs3927686	0.89[JPT][hapmap]
rs3928857	0.89[JPT][hapmap]
rs4425932	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs4462080	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs4618911	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4658039	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs61820915	0.90[ASN][1000 genomes]
rs6428349	0.88[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap]
rs6696801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72732257	0.82[ASN][1000 genomes]
rs72732259	0.82[ASN][1000 genomes]
rs7515074	0.83[CEU][hapmap];0.94[JPT][hapmap]
rs7515472	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7527415	0.82[CEU][hapmap];0.94[JPT][hapmap]
rs7531611	0.89[JPT][hapmap]
rs7535696	0.89[JPT][hapmap]
rs7551077	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs869257	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9427622	0.84[CEU][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap]
rs946750	0.89[JPT][hapmap]
rs946755	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9659527	0.88[CEU][hapmap];0.94[JPT][hapmap];0.89[EUR][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	nsv931415	chr1:196270759-196744780	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1009233	chr1:196301712-196568874	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10494743	CFHR4	cis	cerebellum	SCAN
rs10494743	CFH	cis	parietal	SCAN
rs10494743	CFHR3	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196417400-196428600	Weak transcription	Ovary	ovary
2	chr1:196420000-196460800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr1:196420600-196425600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:196421000-196433400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:196421800-196433400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:196422200-196432200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:196424600-196427800	Weak transcription	Liver	Liver
8	chr1:196424800-196425200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:196425000-196425200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:196425000-196425400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:196425000-196425400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr1:196425000-196425400	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr1:196425000-196425400	Enhancers	Fetal Muscle Leg	muscle
14	chr1:196425000-196425600	Enhancers	HUES64 Cell Line	embryonic stem cell

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