Variant report

Variant	rs9427622
Chromosome Location	chr1:196355524-196355525
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:196355400..196357247-chr1:196358830..196361358,2	K562	blood:
2	chr1:196350682..196352387-chr1:196355306..196358065,2	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10494743	0.84[CEU][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap]
rs10737670	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs10754187	0.94[JPT][hapmap]
rs10754188	0.90[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap]
rs10801530	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10801531	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10801532	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10801533	0.84[CEU][hapmap];0.82[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap]
rs10801537	0.89[JPT][hapmap]
rs10801538	0.84[CEU][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap]
rs10922067	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10922068	0.80[ASN][1000 genomes]
rs10922071	0.83[CHD][hapmap]
rs10922073	0.90[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap]
rs10922075	0.88[JPT][hapmap]
rs10922082	0.89[JPT][hapmap]
rs10922083	0.94[JPT][hapmap]
rs10922084	0.89[JPT][hapmap]
rs10922088	0.83[JPT][hapmap]
rs11807331	0.89[JPT][hapmap]
rs12034150	0.94[JPT][hapmap]
rs12049567	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12065463	0.89[JPT][hapmap]
rs12069983	0.94[JPT][hapmap]
rs12069990	0.94[JPT][hapmap]
rs12121250	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12562176	0.88[CHD][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap]
rs12727032	0.89[JPT][hapmap]
rs12729649	0.94[JPT][hapmap]
rs12756143	0.86[AMR][1000 genomes]
rs1416962	0.88[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap]
rs1538684	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1538686	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1538687	0.94[JPT][hapmap]
rs1769996	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2027368	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2147469	0.83[ASN][1000 genomes]
rs2878551	0.84[CHD][hapmap]
rs2878557	0.94[JPT][hapmap]
rs2878559	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs35582782	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3855964	0.94[JPT][hapmap]
rs3927686	0.94[JPT][hapmap]
rs3928857	0.94[JPT][hapmap]
rs4618911	0.94[JPT][hapmap]
rs4658039	0.94[JPT][hapmap]
rs6428337	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6696801	0.83[CEU][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap]
rs7515074	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7515472	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7527415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7531611	0.94[JPT][hapmap]
rs7535696	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7551077	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs869257	0.94[JPT][hapmap]
rs946750	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs946755	0.94[JPT][hapmap]
rs9659527	0.80[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469680	chr1:196259846-196419016	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv482746	chr1:196259846-196419016	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	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
4	nsv872953	chr1:196286639-196411281	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv1826904	chr1:196291977-196371432	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
6	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
7	nsv872954	chr1:196304863-196387809	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv872955	chr1:196339655-196374780	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
9	nsv548742	chr1:196339655-196391866	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv872956	chr1:196339655-196411281	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv872957	chr1:196347066-196411281	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9427622	CFH	cis	parietal	SCAN
rs9427622	CFHR4	cis	cerebellum	SCAN
rs9427622	RGS1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196343400-196377200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr1:196343600-196362200	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:196343600-196369200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr1:196343800-196362200	Weak transcription	Liver	Liver
5	chr1:196346200-196355600	Weak transcription	Fetal Lung	lung
6	chr1:196349400-196368600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:196355000-196356600	Weak transcription	HSMMtube	muscle

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