Variant report

Variant	rs16840224
Chromosome Location	chr1:196569681-196569682
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	chr1:196569536..196572228-chr1:196576361..196578851,2	K562	blood:

Variant related genes	Relation type
ENSG00000162687	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10494743	0.84[JPT][hapmap]
rs10754187	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs10754188	0.84[JPT][hapmap]
rs10754195	0.81[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs10754196	0.95[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];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10754198	0.90[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10801537	0.86[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10801538	0.84[JPT][hapmap]
rs10801550	0.88[ASN][1000 genomes]
rs10801551	0.95[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs10922071	0.90[CHB][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap]
rs10922073	0.84[JPT][hapmap]
rs10922075	0.90[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs10922082	0.95[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs10922083	0.95[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap]
rs10922084	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs10922088	0.91[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11807331	0.86[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap]
rs12034150	0.86[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs12061508	0.83[ASN][1000 genomes]
rs12065463	0.95[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap]
rs12069983	0.81[CEU][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.92[TSI][hapmap]
rs12069990	0.81[CEU][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.92[TSI][hapmap]
rs12562176	0.84[JPT][hapmap]
rs12727032	0.82[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs12729649	0.83[JPT][hapmap]
rs1416962	0.84[JPT][hapmap]
rs1538687	0.81[CEU][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.90[TSI][hapmap]
rs2878557	0.81[CEU][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.90[TSI][hapmap]
rs34388368	0.81[ASN][1000 genomes]
rs3855964	0.81[CEU][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.92[TSI][hapmap]
rs3927686	0.81[CEU][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.92[TSI][hapmap]
rs3928857	0.81[CEU][hapmap];0.80[GIH][hapmap];0.83[JPT][hapmap]
rs4425932	0.82[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4462080	0.82[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs4618911	0.84[JPT][hapmap]
rs4658039	0.84[JPT][hapmap]
rs61819890	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6428349	0.82[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs6660100	0.82[ASN][1000 genomes]
rs6680396	0.95[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs6690982	0.81[ASN][1000 genomes]
rs6696801	0.84[JPT][hapmap]
rs7531611	0.81[CEU][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.89[TSI][hapmap]
rs7535696	0.81[CEU][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.92[TSI][hapmap]
rs7548553	0.88[ASN][1000 genomes]
rs869257	0.84[JPT][hapmap]
rs946755	0.84[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16840224	CFHR3	cis	parietal	SCAN
rs16840224	CLDN18	trans	parietal	SCAN
rs16840224	CFH	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196557800-196574200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr1:196558000-196574400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:196558400-196574200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:196558400-196575000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:196560600-196571200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:196564000-196575800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:196569400-196572800	Weak transcription	Liver	Liver

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