Variant report

Variant	rs2021394
Chromosome Location	chr5:57653168-57653169
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10035488	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10040280	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10042036	0.84[EUR][1000 genomes]
rs10070290	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10471450	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10472048	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10472049	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10472054	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10472060	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10472061	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12153332	1.00[CHD][hapmap]
rs12188948	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13328216	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1428376	0.89[YRI][hapmap]
rs1477347	0.87[YRI][hapmap]
rs1508904	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17763980	0.83[LWK][hapmap];0.89[YRI][hapmap]
rs17764708	0.91[GIH][hapmap];0.84[TSI][hapmap]
rs17765151	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17765997	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1848512	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2021395	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2047751	0.98[EUR][1000 genomes]
rs27937	0.85[TSI][hapmap]
rs28459538	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28475041	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3846534	0.95[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56242962	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59497655	0.84[EUR][1000 genomes]
rs59595416	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60482268	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6450473	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs72755786	0.80[AFR][1000 genomes]
rs72758116	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72758120	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72758121	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7717376	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7722936	0.80[EUR][1000 genomes]
rs9292159	0.84[EUR][1000 genomes]
rs9292160	0.97[EUR][1000 genomes]
rs984147	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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	esv3489100	chr5:57545689-57669673	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv3489101	chr5:57545689-57669673	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2021394	SKIV2L2	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57649400-57655000	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr5:57650200-57655600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:57650200-57655800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr5:57650400-57655800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:57650400-57656000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:57651800-57656400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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