Variant report

Variant	rs2168363
Chromosome Location	chr11:18258928-18258929
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:18257019-18259896	MCF10A-Er-Src	breast:	n/a	n/a
2	MBD4	chr11:18258171-18258941	HepG2	liver:	n/a	n/a
3	POLR2A	chr11:18255727-18259897	MCF10A-Er-Src	breast:	n/a	n/a
4	TEAD4	chr11:18258065-18259065	HepG2	liver:	n/a	n/a
5	SP1	chr11:18258169-18259040	HepG2	liver:	n/a	n/a
6	CEBPB	chr11:18258220-18258941	HepG2	liver:	n/a	chr11:18258577-18258588
7	FOXA2	chr11:18258353-18259061	HepG2	liver:	n/a	n/a
8	MYBL2	chr11:18258080-18259057	HepG2	liver:	n/a	n/a
9	FOXA1	chr11:18258189-18259006	HepG2	liver:	n/a	n/a
10	NFIC	chr11:18258226-18259068	HepG2	liver:	n/a	n/a
11	EP300	chr11:18258312-18259055	HepG2	liver:	n/a	n/a
12	JUND	chr11:18258554-18258999	HepG2	liver:	n/a	n/a
13	FOXA1	chr11:18258210-18258934	HepG2	liver:	n/a	n/a
14	JUN	chr11:18258405-18258982	HepG2	liver:	n/a	chr11:18258805-18258818
15	EP300	chr11:18258134-18258997	HepG2	liver:	n/a	n/a
16	ARID3A	chr11:18258031-18259202	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
SAA4	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10766463	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832904	1.00[JPT][hapmap]
rs10832908	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024553	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs11024561	0.83[EUR][1000 genomes]
rs11024563	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024566	0.80[AMR][1000 genomes]
rs11024574	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11024576	0.85[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11024577	0.81[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11024578	1.00[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12361253	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12364058	0.82[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs2445145	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2445175	0.92[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2445176	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2468779	0.84[EUR][1000 genomes]
rs2468790	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs2468856	0.84[EUR][1000 genomes]
rs2925145	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4757627	1.00[JPT][hapmap]
rs4757628	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757629	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757630	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56310011	0.84[EUR][1000 genomes]
rs67006796	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67712345	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7103794	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7117484	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7117890	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72881516	0.80[AMR][1000 genomes]
rs7935726	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv428569	chr11:18194030-18350869	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2168363	PIK3C2A	cis	parietal	SCAN
rs2168363	LDHC	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18258000-18259400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr11:18258800-18259200	Flanking Active TSS	Liver	Liver
3	chr11:18258800-18262800	Enhancers	HepG2	liver
4	chr11:18258800-18265800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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