Variant report

Variant	rs12065463
Chromosome Location	chr1:196464754-196464755
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	chr1:196458697..196461420-chr1:196463118..196465418,4	K562	blood:
2	chr1:196462288..196467297-chr1:196468697..196474104,7	K562	blood:

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10494743	0.83[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs10737670	0.86[CEU][hapmap];0.94[JPT][hapmap]
rs10754187	0.86[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs10754188	0.82[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs10754195	0.83[JPT][hapmap]
rs10754196	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap]
rs10754198	0.95[CEU][hapmap]
rs10801530	0.85[CEU][hapmap];0.94[JPT][hapmap]
rs10801531	0.81[CEU][hapmap];0.94[JPT][hapmap]
rs10801532	0.84[GIH][hapmap];0.94[JPT][hapmap];0.92[TSI][hapmap]
rs10801533	0.89[JPT][hapmap]
rs10801534	0.81[EUR][1000 genomes]
rs10801535	0.83[EUR][1000 genomes]
rs10801537	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10801538	0.83[CHD][hapmap];0.94[JPT][hapmap]
rs10801539	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10801551	0.91[CHB][hapmap]
rs10922066	0.82[EUR][1000 genomes]
rs10922071	0.88[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10922073	0.82[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10922075	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10922078	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10922082	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10922083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10922084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10922088	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs11576790	0.92[ASN][1000 genomes]
rs11807331	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12034150	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs12049567	0.89[JPT][hapmap]
rs12065519	0.92[ASN][1000 genomes]
rs12069983	0.85[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs12069990	0.86[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs12123128	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12562176	0.82[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs12727032	0.89[JPT][hapmap]
rs12729649	0.85[CEU][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes]
rs1416962	0.86[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1538685	0.81[EUR][1000 genomes]
rs1538686	0.81[CHD][hapmap];0.89[JPT][hapmap]
rs1538687	0.86[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs16840224	0.95[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap]
rs1769996	0.86[CEU][hapmap];0.94[JPT][hapmap]
rs1832617	0.86[ASN][1000 genomes]
rs2027368	0.86[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.92[TSI][hapmap]
rs2878557	0.86[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs2878558	0.81[EUR][1000 genomes]
rs2878559	0.89[JPT][hapmap]
rs3855964	0.86[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs3927686	0.86[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs3928857	0.85[CEU][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap]
rs4425932	0.83[JPT][hapmap]
rs4462080	0.83[JPT][hapmap]
rs4618911	0.82[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs4658039	0.82[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs60495441	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61820915	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6428349	0.83[JPT][hapmap]
rs6678457	0.81[EUR][1000 genomes]
rs6680396	0.91[CHB][hapmap]
rs6696801	0.83[CHD][hapmap];0.94[JPT][hapmap]
rs6697795	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72732257	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72732259	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7515074	0.89[JPT][hapmap]
rs7527415	0.89[JPT][hapmap]
rs7531611	0.86[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs7535696	0.86[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.92[TSI][hapmap]
rs7550015	0.81[EUR][1000 genomes]
rs869257	0.82[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs9427622	0.89[JPT][hapmap]
rs946750	0.86[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap]
rs946755	0.82[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs9659527	0.88[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12065463	CFH	cis	parietal	SCAN
rs12065463	CLDN18	trans	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196436400-196485200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:196437400-196467800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:196447800-196468000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr1:196451400-196467600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr1:196452800-196471200	Weak transcription	Liver	Liver
6	chr1:196454400-196467400	Weak transcription	Ovary	ovary
7	chr1:196462600-196465800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:196463200-196466400	Active TSS	K562	blood

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