Variant report

Variant	rs28360522
Chromosome Location	chr22:28528745-28528746
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs13054964	0.82[CEU][hapmap];0.95[EUR][1000 genomes]
rs13055218	0.95[EUR][1000 genomes]
rs13055244	0.85[EUR][1000 genomes]
rs13055409	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13055548	0.81[EUR][1000 genomes]
rs13056121	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13056319	0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs13057007	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13057353	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs13057692	0.80[AFR][1000 genomes]
rs13057948	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs13058493	0.82[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs135113	0.82[CEU][hapmap]
rs135642	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]
rs1569700	0.82[CEU][hapmap];0.82[AFR][1000 genomes]
rs34013124	0.98[EUR][1000 genomes]
rs34031771	0.81[EUR][1000 genomes]
rs34189918	1.00[EUR][1000 genomes]
rs34262300	0.82[AFR][1000 genomes]
rs34364992	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34625726	1.00[EUR][1000 genomes]
rs34925495	0.80[AFR][1000 genomes]
rs34946887	0.88[EUR][1000 genomes]
rs35051985	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs35098100	0.98[EUR][1000 genomes]
rs35182834	0.83[EUR][1000 genomes]
rs35286067	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35417721	0.80[EUR][1000 genomes]
rs35568348	0.88[EUR][1000 genomes]
rs35568804	0.81[EUR][1000 genomes]
rs35649017	0.95[EUR][1000 genomes]
rs35750499	0.81[EUR][1000 genomes]
rs35906248	0.95[EUR][1000 genomes]
rs36060887	0.84[EUR][1000 genomes]
rs41281591	0.83[EUR][1000 genomes]
rs71325266	0.81[EUR][1000 genomes]
rs71325269	0.93[EUR][1000 genomes]
rs71325273	0.95[EUR][1000 genomes]
rs71325275	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71325276	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7285440	0.82[CEU][hapmap];1.00[MEX][hapmap]
rs736531	0.88[EUR][1000 genomes]
rs767919	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8141981	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8142398	0.87[AFR][1000 genomes]
rs910009	0.98[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28360522	SIX3	trans	lymphoblastoid	seeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28502400-28535800	Weak transcription	Right Ventricle	heart
2	chr22:28513200-28538000	Weak transcription	Dnd41	blood
3	chr22:28516800-28532600	Weak transcription	Aorta	Aorta
4	chr22:28516800-28534600	Weak transcription	Fetal Brain Female	brain
5	chr22:28517800-28533000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr22:28525800-28533000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr22:28526000-28530800	Weak transcription	Osteobl	bone
8	chr22:28526400-28529400	Weak transcription	Ovary	ovary
9	chr22:28526600-28529400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr22:28528200-28529000	Weak transcription	Fetal Intestine Small	intestine
11	chr22:28528200-28535200	Weak transcription	Fetal Heart	heart

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