Variant report

Variant	rs9613568
Chromosome Location	chr22:28531088-28531089
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11090520	0.93[EUR][1000 genomes]
rs17409195	0.90[GIH][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap]
rs17483415	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs738455	0.84[EUR][1000 genomes]
rs738474	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs9608663	0.91[EUR][1000 genomes]
rs9608665	0.82[EUR][1000 genomes]
rs9608666	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9608672	0.86[EUR][1000 genomes]
rs9608675	0.90[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs9613549	0.84[EUR][1000 genomes]
rs9613552	0.82[EUR][1000 genomes]
rs9613558	0.87[EUR][1000 genomes]
rs9613560	0.88[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs9613564	0.83[EUR][1000 genomes]
rs9613569	0.88[GIH][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.97[EUR][1000 genomes]
rs9613573	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs9613575	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9613589	1.00[AFR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9613568	TTC28AS	cis	cerebellum	SCAN
rs9613568	HPS4	cis	parietal	SCAN
rs9613568	CRYBB2P1	cis	parietal	SCAN
rs9613568	SF3A1	cis	cerebellum	SCAN

Chromatin state (count:16 , 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	chr22:28528200-28535200	Weak transcription	Fetal Heart	heart
8	chr22:28529600-28535800	Weak transcription	Ovary	ovary
9	chr22:28530000-28535800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr22:28530200-28532600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr22:28530200-28532600	Weak transcription	Fetal Lung	lung
12	chr22:28530800-28531200	Enhancers	Osteobl	bone
13	chr22:28530800-28531600	Enhancers	NHDF-Ad	bronchial
14	chr22:28531000-28531200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
15	chr22:28531000-28531200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr22:28531000-28531600	Enhancers	NHLF	lung

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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