Variant report

Variant	rs9613574
Chromosome Location	chr22:28604583-28604584
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1072967	1.00[YRI][hapmap]
rs11912165	1.00[YRI][hapmap]
rs17502181	1.00[CEU][hapmap]
rs2056962	1.00[CEU][hapmap]
rs2223369	1.00[CEU][hapmap]
rs2346395	1.00[CEU][hapmap]
rs5752710	0.81[CHB][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs5762498	1.00[YRI][hapmap]
rs5762532	0.81[CHB][hapmap]
rs5762541	0.81[CHB][hapmap]
rs9608667	0.81[CHB][hapmap]
rs9608677	1.00[CEU][hapmap]
rs9613580	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9613581	0.80[EUR][1000 genomes]
rs9613588	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv962867	chr22:28595811-28611386	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9613574	TTC28	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28600200-28616400	Weak transcription	Ovary	ovary
2	chr22:28602600-28604600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr22:28602800-28604600	Enhancers	Muscle Satellite Cultured Cells	--
4	chr22:28603000-28604600	Enhancers	NH-A	brain
5	chr22:28603000-28605400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr22:28603200-28604600	Enhancers	Osteobl	bone
7	chr22:28603200-28605200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr22:28603600-28604600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr22:28603600-28604600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr22:28603600-28604600	Enhancers	NHEK	skin
11	chr22:28603600-28605800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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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

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