Variant report

Variant	rs7556879
Chromosome Location	chr2:212465328-212465329
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10203022	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10204337	0.94[ASN][1000 genomes]
rs10210942	0.84[EUR][1000 genomes]
rs10932387	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10932388	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11684753	0.86[ASN][1000 genomes]
rs12465773	0.84[EUR][1000 genomes]
rs12694244	0.89[ASN][1000 genomes]
rs1829611	0.81[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs1851196	0.93[ASW][hapmap];0.92[TSI][hapmap]
rs1972142	0.81[CEU][hapmap]
rs1972143	0.81[ASW][hapmap];0.81[CEU][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs4488593	0.82[CEU][hapmap]
rs4539738	0.91[ASN][1000 genomes]
rs6746549	0.92[ASN][1000 genomes]
rs7559679	0.83[TSI][hapmap]
rs7559734	0.98[ASN][1000 genomes]
rs7585825	0.89[ASN][1000 genomes]
rs7586137	0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7589006	0.81[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs7602185	0.93[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7602757	0.87[ASN][1000 genomes]
rs7602850	0.87[ASN][1000 genomes]
rs9288434	0.84[EUR][1000 genomes]
rs9288435	0.93[ASW][hapmap];0.81[CEU][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs9288436	0.92[TSI][hapmap]
rs939591	0.91[ASN][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	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
2	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
3	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
rs7556879	CPS1IT1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:212452400-212466800	Weak transcription	Aorta	Aorta
2	chr2:212456600-212473600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:212462600-212465800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:212462800-212465800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:212463600-212465400	Enhancers	Fetal Heart	heart

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