Variant report

Variant	rs12504448
Chromosome Location	chr4:74369406-74369407
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10004505	0.82[EUR][1000 genomes]
rs10016403	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10019146	0.87[TSI][hapmap]
rs10028196	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10028276	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10212657	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10213305	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10805065	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10938077	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10938078	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10938079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10938085	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10938086	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1158101	0.85[ASN][1000 genomes]
rs1159624	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11728915	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11733262	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11935001	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11939341	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11943798	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12503916	0.87[TSI][hapmap]
rs12507775	0.87[TSI][hapmap]
rs12508974	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12510629	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13103378	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13107306	0.83[ASN][1000 genomes]
rs13120998	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13124940	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13144296	0.81[CEU][hapmap]
rs13150405	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13353732	0.92[EUR][1000 genomes]
rs1358592	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs1528924	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1569204	0.83[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1590115	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1590116	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16849461	0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16849484	0.83[ASN][1000 genomes]
rs16849508	0.85[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs16849628	0.87[TSI][hapmap]
rs16849727	0.86[CEU][hapmap];0.93[TSI][hapmap]
rs1881611	0.92[EUR][1000 genomes]
rs1894293	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1919469	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1919479	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1997332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997333	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040354	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2071097	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071098	0.83[ASN][1000 genomes]
rs2141465	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2141470	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2178290	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178292	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2204736	0.94[ASN][1000 genomes]
rs28838047	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34238679	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34468776	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35233345	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35988516	0.96[ASN][1000 genomes]
rs3765639	0.81[ASN][1000 genomes]
rs4235119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4267703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4267704	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4267705	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4438732	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4574378	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4618279	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4631010	0.95[ASN][1000 genomes]
rs4694170	0.82[CEU][hapmap]
rs4694173	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56011127	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56384466	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6446937	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446939	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6446941	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6852149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6852772	0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs72647083	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7676460	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7682201	0.87[TSI][hapmap]
rs9990707	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9997572	0.82[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	esv3430875	chr4:74243646-74420354	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12504448	CXCL2	cis	cerebellum	SCAN
rs12504448	ART3	cis	cerebellum	SCAN
rs12504448	MUC7	cis	cerebellum	SCAN
rs12504448	ANKRD17	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74361800-74371800	Genic enhancers	Liver	Liver
2	chr4:74366600-74372400	Weak transcription	Fetal Intestine Small	intestine
3	chr4:74366600-74373000	Weak transcription	Fetal Intestine Large	intestine
4	chr4:74368400-74372200	Weak transcription	HepG2	liver

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