Variant report

Variant	rs10514894
Chromosome Location	chr5:59658798-59658799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10514893	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1345782	0.87[CHD][hapmap];0.88[JPT][hapmap]
rs1423471	1.00[CEU][hapmap]
rs16877896	1.00[CEU][hapmap]
rs16877898	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs16877901	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs16877933	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16877936	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16877964	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16877967	1.00[CEU][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes]
rs16877993	0.88[JPT][hapmap]
rs16878035	1.00[CEU][hapmap];1.00[MEX][hapmap];0.85[EUR][1000 genomes]
rs16878037	1.00[CEU][hapmap];1.00[MEX][hapmap];0.85[EUR][1000 genomes]
rs16878086	1.00[CEU][hapmap];1.00[MEX][hapmap];0.85[EUR][1000 genomes]
rs16878104	1.00[CEU][hapmap]
rs16878106	1.00[CEU][hapmap]
rs17326404	1.00[CEU][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17378750	1.00[CEU][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1862589	1.00[CEU][hapmap];1.00[MEX][hapmap];0.85[EUR][1000 genomes]
rs1895412	0.96[ASN][1000 genomes]
rs3763059	1.00[CEU][hapmap]
rs4090603	1.00[CEU][hapmap]
rs4130444	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4580738	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs55952213	0.88[EUR][1000 genomes]
rs56151644	0.85[EUR][1000 genomes]
rs56217581	0.85[EUR][1000 genomes]
rs56247947	0.96[EUR][1000 genomes]
rs56262275	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57177718	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58376959	0.85[EUR][1000 genomes]
rs58512371	0.96[EUR][1000 genomes]
rs58594585	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58704174	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58891299	0.85[EUR][1000 genomes]
rs59014679	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59576667	0.96[EUR][1000 genomes]
rs59578756	0.96[EUR][1000 genomes]
rs60104228	0.85[EUR][1000 genomes]
rs60962155	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61474228	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6860277	0.88[JPT][hapmap]
rs6878429	1.00[CEU][hapmap]
rs6881782	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6886304	0.88[JPT][hapmap]
rs6886423	0.92[EUR][1000 genomes]
rs73106781	0.96[EUR][1000 genomes]
rs73106782	0.96[EUR][1000 genomes]
rs73108618	0.82[ASN][1000 genomes]
rs73108627	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73108631	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73759052	0.85[EUR][1000 genomes]
rs73759053	0.85[EUR][1000 genomes]
rs7702188	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7723861	1.00[CEU][hapmap]
rs7725629	1.00[CEU][hapmap];0.85[EUR][1000 genomes]

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	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv830316	chr5:59480269-59689829	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10514894	CXCL11	trans	brain	seeQTL
rs10514894	CXCL10	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59647200-59694200	Weak transcription	Primary B cells from cord blood	blood
2	chr5:59649400-59668200	Weak transcription	Gastric	stomach
3	chr5:59650400-59674800	Weak transcription	Aorta	Aorta
4	chr5:59657400-59660000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:59658000-59663600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:59658200-59665600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:59658400-59662000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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