Variant report

Variant	rs55913295
Chromosome Location	chr18:9411912-9411913
allele	G/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:14)

rs_ID	r²[population]
rs16955061	0.82[AMR][1000 genomes]
rs34741369	0.82[AMR][1000 genomes]
rs4503865	0.81[EUR][1000 genomes]
rs4797368	0.81[EUR][1000 genomes]
rs4797371	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55637024	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55755093	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55767805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56124420	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6506663	0.81[EUR][1000 genomes]
rs8089405	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8096040	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9748605	0.82[AMR][1000 genomes]
rs9962807	0.81[EUR][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	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1056407	chr18:9144345-9553764	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1062025	chr18:9287249-9552470	Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv543643	chr18:9287249-9552470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv833585	chr18:9401630-9597291	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv428005	chr18:9401658-9542396	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs55913295	TWSG1	cis	Artery Tibial	GTEx
rs55913295	TWSG1	cis	Thyroid	GTEx
rs55913295	TWSG1	cis	Esophagus Muscularis	GTEx
rs55913295	TWSG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9388800-9413200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr18:9396600-9413800	Weak transcription	NH-A	brain
3	chr18:9397200-9413600	Weak transcription	HSMMtube	muscle
4	chr18:9397200-9416800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr18:9397800-9416600	Weak transcription	HSMM	muscle
6	chr18:9399600-9413600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr18:9400600-9413400	Weak transcription	Osteobl	bone
8	chr18:9400600-9416600	Weak transcription	Brain Anterior Caudate	brain
9	chr18:9401400-9413800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr18:9401600-9413600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr18:9404000-9413000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr18:9404000-9416800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr18:9405000-9412600	Weak transcription	Fetal Stomach	stomach
14	chr18:9405000-9417000	Weak transcription	Right Atrium	heart
15	chr18:9405600-9417400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr18:9406400-9413400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr18:9406400-9414800	Weak transcription	H1 Derived Mesenchymal Stem 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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