Variant report

Variant	rs12619171
Chromosome Location	chr2:212446818-212446819
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1009142	0.85[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[ASN][1000 genomes]
rs10198754	0.87[EUR][1000 genomes]
rs10203022	0.83[GIH][hapmap];0.94[MKK][hapmap]
rs10210942	0.86[ASN][1000 genomes]
rs10804199	0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs10932386	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11679779	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11679860	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11684753	0.99[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11687988	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11691078	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11695852	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12465773	0.84[ASN][1000 genomes]
rs12614500	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12694243	0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694244	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12694245	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13007756	0.94[ASN][1000 genomes]
rs1818751	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1829610	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs1829611	0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1965462	0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs1972142	1.00[JPT][hapmap]
rs1972143	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1976834	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2371303	0.92[ASN][1000 genomes]
rs2371304	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2371305	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2888004	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4488593	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4539738	0.94[EUR][1000 genomes]
rs4599046	0.85[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4640322	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672619	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]
rs4673623	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs4673624	0.93[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6721804	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6731454	0.90[ASN][1000 genomes]
rs7561282	0.83[ASW][hapmap];0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7572669	0.92[ASN][1000 genomes]
rs7585825	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7586137	0.83[ASW][hapmap];0.86[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7589006	0.94[ASW][hapmap];0.86[CEU][hapmap];0.94[TSI][hapmap];0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7595207	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595223	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602185	0.83[GIH][hapmap]
rs9288434	0.82[ASN][1000 genomes]
rs9288435	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9288436	0.83[MKK][hapmap]
rs939591	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000722	chr2:212272622-212465143	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv460069	chr2:212415948-212471642	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv584320	chr2:212415948-212471642	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv584321	chr2:212446818-212511895	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12619171	CPS1IT1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:212419400-212451800	Weak transcription	Aorta	Aorta
2	chr2:212435400-212450000	Weak transcription	Fetal Heart	heart
3	chr2:212444400-212451200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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