Variant report

Variant	rs12562176
Chromosome Location	chr1:196521049-196521050
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:196508225..196510661-chr1:196517762..196521864,3	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10494743	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]
rs10737670	0.89[JPT][hapmap]
rs10754187	0.89[JPT][hapmap]
rs10754188	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10754195	0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10754196	0.84[JPT][hapmap]
rs10801530	0.89[JPT][hapmap]
rs10801531	0.89[JPT][hapmap]
rs10801532	0.89[JPT][hapmap]
rs10801533	0.83[CEU][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap]
rs10801537	0.94[JPT][hapmap]
rs10801538	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];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10801550	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10922071	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs10922073	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10922075	0.86[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs10922078	0.91[ASN][1000 genomes]
rs10922082	0.81[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs10922083	0.82[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs10922084	0.82[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs10922088	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs11576790	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11807331	0.94[JPT][hapmap]
rs12034150	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12049567	0.94[JPT][hapmap]
rs12065463	0.82[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs12065519	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12069983	0.89[JPT][hapmap]
rs12069990	0.89[JPT][hapmap]
rs12123128	0.86[ASN][1000 genomes]
rs12727032	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12729649	0.89[JPT][hapmap]
rs1416962	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1538686	0.91[CHD][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap]
rs1538687	0.89[JPT][hapmap]
rs16840224	0.84[JPT][hapmap]
rs1769996	0.89[JPT][hapmap]
rs1832617	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2027368	0.89[JPT][hapmap]
rs2878551	0.91[CHD][hapmap]
rs2878557	0.89[JPT][hapmap]
rs2878559	0.83[CEU][hapmap];0.94[JPT][hapmap]
rs3855964	0.89[JPT][hapmap]
rs3927686	0.89[JPT][hapmap]
rs3928857	0.89[JPT][hapmap]
rs4425932	0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4462080	0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4618911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4658039	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs60495441	0.89[ASN][1000 genomes]
rs6428349	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6696801	0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs6697795	0.89[ASN][1000 genomes]
rs72732257	0.84[ASN][1000 genomes]
rs72732259	0.81[ASN][1000 genomes]
rs7515074	0.94[JPT][hapmap]
rs7527415	0.94[JPT][hapmap]
rs7531611	0.89[JPT][hapmap]
rs7535696	0.89[JPT][hapmap]
rs7548553	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs869257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9427622	0.88[CHD][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap]
rs946750	0.89[JPT][hapmap]
rs946755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9659527	0.87[CEU][hapmap];0.94[JPT][hapmap]

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
rs12562176	CFHR4	cis	cerebellum	SCAN
rs12562176	CFH	cis	parietal	SCAN
rs12562176	CFHR3	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196509800-196529600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr1:196513200-196522400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:196514600-196527600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:196516200-196526600	Weak transcription	Liver	Liver
5	chr1:196521000-196527000	Weak transcription	NHDF-Ad	bronchial

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