Variant report

Variant	rs134170
Chromosome Location	chr22:28612645-28612646
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs134169	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134174	0.86[JPT][hapmap];0.84[AFR][1000 genomes]
rs134184	0.94[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs134185	0.82[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs134187	0.96[LWK][hapmap];0.84[AFR][1000 genomes]
rs135640	0.89[LWK][hapmap]
rs16986354	0.88[LWK][hapmap];1.00[YRI][hapmap]
rs2073029	0.83[CEU][hapmap];0.90[GIH][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap]
rs4820782	0.86[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs5762481	0.82[ASW][hapmap];0.89[CEU][hapmap];0.93[LWK][hapmap];0.88[TSI][hapmap]
rs73168154	0.81[AFR][1000 genomes]
rs9608667	0.84[LWK][hapmap]

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	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
2	nsv459866	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv588879	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs134170	TTC28	cis	cerebellum	SCAN
rs134170	GNAZ	cis	cerebellum	SCAN
rs134170	SUSD2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28600200-28616400	Weak transcription	Ovary	ovary
2	chr22:28604600-28617800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr22:28611800-28616400	Weak transcription	Left Ventricle	heart
4	chr22:28612200-28625600	Weak transcription	Aorta	Aorta
5	chr22:28612200-28634800	Weak transcription	Dnd41	blood
6	chr22:28612600-28616400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

Quick Search:

Input of quick search could be:

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

what's new

Quick links