Variant report

Variant	rs16988966
Chromosome Location	chr22:31078457-31078458
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11703133	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11703252	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13053148	0.81[AMR][1000 genomes]
rs13053186	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13053277	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13054609	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13055971	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13056033	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13057481	0.81[AMR][1000 genomes]
rs13058171	0.81[AMR][1000 genomes]
rs35317322	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41279967	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57114503	0.90[AFR][1000 genomes]
rs71331258	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71331260	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71331261	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71331262	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8142472	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8142842	0.84[AMR][1000 genomes];0.95[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	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv834175	chr22:30976624-31089545	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16988966	TTC28	cis	cerebellum	SCAN
rs16988966	PLA2G3	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31074600-31081400	Weak transcription	Fetal Intestine Small	intestine
2	chr22:31077400-31089800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr22:31077400-31090000	Weak transcription	Fetal Heart	heart
4	chr22:31077600-31081200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr22:31077600-31090000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr22:31078200-31081000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr22:31078200-31089200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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