Variant report

Variant	rs738748
Chromosome Location	chr22:28993183-28993184
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11090535	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12163268	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1534884	0.81[AFR][1000 genomes]
rs17507045	0.90[LWK][hapmap]
rs2180460	0.94[LWK][hapmap];1.00[YRI][hapmap]
rs2224337	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57071456	0.90[ASN][1000 genomes]
rs5762702	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762713	0.88[LWK][hapmap]
rs5762734	0.87[LWK][hapmap]
rs5762737	1.00[YRI][hapmap]
rs60410397	0.95[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs72617287	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs72617288	0.93[AFR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067544	chr22:28755418-29055246	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv544674	chr22:28755418-29055246	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv588880	chr22:28807277-29001789	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv459867	chr22:28993183-29109036	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv588881	chr22:28993183-29109036	Weak transcription Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs738748	TTC28AS	cis	cerebellum	SCAN
rs738748	ZDHHC8P1	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28956800-28993200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr22:28967800-28997600	Weak transcription	HepG2	liver
3	chr22:28979200-28993600	Weak transcription	Fetal Stomach	stomach
4	chr22:28990600-28993200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr22:28990600-28994000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr22:28991000-28993800	Enhancers	Osteobl	bone
7	chr22:28991200-28993400	Enhancers	A549	lung
8	chr22:28991200-28996000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr22:28991200-28996200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr22:28991400-28993200	Weak transcription	Colon Smooth Muscle	Colon
11	chr22:28991400-29000800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr22:28991400-29001000	Weak transcription	Fetal Lung	lung
13	chr22:28991400-29003600	Weak transcription	NHLF	lung
14	chr22:28991400-29004200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr22:28991800-29007600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr22:28992800-28993200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr22:28992800-28993600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr22:28993000-28993800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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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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