Variant report

Variant	rs3927686
Chromosome Location	chr1:196385649-196385650
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	chr1:196373223..196374737-chr1:196383662..196386245,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10494743	0.89[JPT][hapmap]
rs10737670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10754187	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10754188	0.89[JPT][hapmap]
rs10754196	0.86[CEU][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.92[TSI][hapmap]
rs10754198	0.81[CEU][hapmap]
rs10801530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10801531	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10801532	0.80[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10801533	0.86[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs10801534	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10801535	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10801537	0.95[CEU][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes]
rs10801538	0.89[JPT][hapmap]
rs10801539	0.86[EUR][1000 genomes]
rs10922066	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10922067	0.84[ASN][1000 genomes]
rs10922068	0.95[ASN][1000 genomes]
rs10922071	0.87[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs10922073	0.89[JPT][hapmap]
rs10922075	0.81[CEU][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes]
rs10922082	0.86[CEU][hapmap];0.94[JPT][hapmap];0.92[TSI][hapmap]
rs10922083	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs10922084	0.86[CEU][hapmap];0.94[JPT][hapmap]
rs10922088	0.89[JPT][hapmap]
rs11807331	0.95[CEU][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs12034150	0.87[JPT][hapmap]
rs12049567	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs12065463	0.86[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs12069983	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12069990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12121250	0.84[ASN][1000 genomes]
rs12562176	0.89[JPT][hapmap]
rs12727032	0.83[JPT][hapmap]
rs12729649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12738109	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1416962	0.89[JPT][hapmap]
rs1538684	0.84[ASN][1000 genomes]
rs1538685	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1538686	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1538687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16840224	0.81[CEU][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.92[TSI][hapmap]
rs1769996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2027368	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2147469	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2878557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2878558	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2878559	0.86[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs35582782	0.84[ASN][1000 genomes]
rs3855964	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];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3928857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4618911	0.89[JPT][hapmap]
rs4658039	0.89[JPT][hapmap]
rs61820915	0.86[EUR][1000 genomes]
rs6678457	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696801	0.89[JPT][hapmap]
rs72732257	0.82[EUR][1000 genomes]
rs7515074	0.94[JPT][hapmap]
rs7515472	0.84[ASN][1000 genomes]
rs7527415	0.94[JPT][hapmap]
rs7531611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7535696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7550015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7551077	0.84[ASN][1000 genomes]
rs869257	0.89[JPT][hapmap]
rs9427622	0.94[JPT][hapmap]
rs946750	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs946755	0.89[JPT][hapmap]
rs9659527	0.86[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
6	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
7	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
8	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
9	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
rs3927686	CFHR3	cis	parietal	SCAN
rs3927686	CFH	cis	parietal	SCAN
rs3927686	CLDN18	trans	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196358000-196393800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr1:196377200-196398600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:196377600-196390000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:196377600-196392800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:196377600-196403200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:196377800-196402800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:196378000-196393600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:196378200-196400200	Weak transcription	Fetal Kidney	kidney
9	chr1:196383800-196398800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:196384200-196387600	Weak transcription	Ovary	ovary
11	chr1:196384400-196393000	Weak transcription	Liver	Liver

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