Variant report

Variant	rs6428349
Chromosome Location	chr1:196575602-196575603
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10494743	0.88[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap]
rs10754188	0.91[CEU][hapmap];0.95[CHB][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap]
rs10754195	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10754196	0.82[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs10754198	0.89[ASN][1000 genomes]
rs10801533	0.83[JPT][hapmap];0.88[TSI][hapmap]
rs10801537	0.83[JPT][hapmap]
rs10801538	0.88[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap]
rs10801550	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10922073	0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap]
rs10922075	0.83[JPT][hapmap]
rs10922082	0.83[JPT][hapmap]
rs10922083	0.82[JPT][hapmap]
rs10922084	0.83[JPT][hapmap]
rs10922088	0.91[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs11807331	0.83[JPT][hapmap]
rs12034150	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12049567	0.83[JPT][hapmap]
rs12065463	0.83[JPT][hapmap]
rs12562176	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]
rs12727032	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1416962	0.91[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap]
rs1538686	0.82[GIH][hapmap];0.83[JPT][hapmap];0.82[TSI][hapmap]
rs16840224	0.82[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2878559	0.83[JPT][hapmap]
rs4425932	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4462080	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4618911	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs4658039	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs61819890	0.87[ASN][1000 genomes]
rs6696801	0.91[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.98[TSI][hapmap]
rs7548553	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs869257	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs946755	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs9659527	0.82[CEU][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv947214	chr1:196573327-196578627	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6428349	CFHR3	cis	parietal	SCAN
rs6428349	CFH	cis	parietal	SCAN
rs6428349	CFHR4	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196564000-196575800	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr1:196570800-196575800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:196572600-196575800	Weak transcription	Fetal Kidney	kidney
4	chr1:196573400-196576600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:196573400-196577000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:196574600-196576000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:196574600-196576200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:196574600-196576800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:196574800-196575800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:196574800-196575800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr1:196574800-196578600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:196574800-196578800	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr1:196575000-196575800	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr1:196575200-196575800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:196575200-196576600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr1:196575400-196576000	Weak transcription	Ovary	ovary
17	chr1:196575400-196576400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:196575400-196576600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr1:196575600-196575800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:196575600-196576200	Flanking Active TSS	Liver	Liver

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