Variant report

Variant	rs6696801
Chromosome Location	chr1:196433384-196433385
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10494743	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]
rs10737670	0.89[JPT][hapmap]
rs10754187	0.89[JPT][hapmap]
rs10754188	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[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	0.91[CEU][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs10801537	0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs10801538	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];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10801539	0.90[ASN][1000 genomes]
rs10922067	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10922068	0.89[EUR][1000 genomes]
rs10922071	0.86[CHB][hapmap];0.88[CHD][hapmap];0.93[ASN][1000 genomes]
rs10922073	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10922075	0.94[JPT][hapmap]
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	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11807331	0.82[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs12034150	0.91[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs12049567	0.83[CEU][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12065463	0.83[CHD][hapmap];0.94[JPT][hapmap]
rs12065519	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12069983	0.89[JPT][hapmap]
rs12069990	0.89[JPT][hapmap]
rs12121250	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12562176	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]
rs12727032	0.91[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs12729649	0.89[JPT][hapmap]
rs1416962	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1538684	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1538686	0.98[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1538687	0.89[JPT][hapmap]
rs16840224	0.84[JPT][hapmap]
rs1769996	0.89[JPT][hapmap]
rs1832617	0.90[EUR][1000 genomes]
rs2027368	0.89[JPT][hapmap]
rs2878551	0.84[CHD][hapmap]
rs2878557	0.89[JPT][hapmap]
rs2878559	0.91[CEU][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes]
rs35582782	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3855964	0.89[JPT][hapmap]
rs3927686	0.89[JPT][hapmap]
rs3928857	0.89[JPT][hapmap]
rs4425932	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs4462080	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs4618911	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs4658039	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs61820915	0.93[ASN][1000 genomes]
rs6428349	0.91[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.98[TSI][hapmap]
rs7515074	0.82[CEU][hapmap];0.94[JPT][hapmap]
rs7515472	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7527415	0.81[CEU][hapmap];0.94[JPT][hapmap]
rs7531611	0.89[JPT][hapmap]
rs7535696	0.89[JPT][hapmap]
rs7551077	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs869257	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs9427622	0.83[CEU][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap]
rs946750	0.89[JPT][hapmap]
rs946755	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs9659527	0.87[CEU][hapmap];0.94[JPT][hapmap];0.88[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
rs6696801	CFHR3	cis	parietal	SCAN
rs6696801	CFH	cis	parietal	SCAN
rs6696801	CFHR4	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196420000-196460800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:196421000-196433400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr1:196421800-196433400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr1:196425400-196433800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:196425400-196434000	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:196429000-196433600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:196429000-196435600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:196429200-196435400	Weak transcription	Ovary	ovary
9	chr1:196429200-196450400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:196430800-196439600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:196431200-196433600	Weak transcription	Fetal Kidney	kidney
12	chr1:196431600-196433400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:196431600-196433600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:196432000-196434600	Strong transcription	Liver	Liver
15	chr1:196432200-196437400	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:196432800-196434200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:196433200-196436000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:196433200-196436400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:196433200-196437000	Strong transcription	HUES64 Cell Line	embryonic stem cell

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