Variant report

Variant	rs12523073
Chromosome Location	chr5:49449531-49449532
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10053631	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10053639	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10940533	0.81[ASN][1000 genomes]
rs11740458	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11950949	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11953045	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2168922	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2353222	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4249603	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4446513	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4865550	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4865552	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4865727	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4865801	0.80[ASN][1000 genomes]
rs55815545	0.87[AFR][1000 genomes]
rs8188099	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs8188203	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9688258	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv19415	chr5:49405763-49485157	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	n/a	n/a	inside rSNPs	diseases
2	nsv820439	chr5:49405763-49552643	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	esv15107	chr5:49405763-49562327	Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv2760950	chr5:49432831-49624358	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv598089	chr5:49441601-49547088	ZNF genes & repeats Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv598090	chr5:49441966-49514368	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	diseases
7	nsv598091	chr5:49441966-49547088	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv830285	chr5:49445361-49527825	ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv598092	chr5:49448027-49514368	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12523073	EMB	cis	Thyroid	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49441400-49450400	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr5:49441400-49450400	Weak transcription	Hela-S3	cervix
3	chr5:49441400-49450400	Weak transcription	NH-A	brain
4	chr5:49441400-49450400	Weak transcription	NHEK	skin
5	chr5:49441400-49450400	Weak transcription	Osteobl	bone
6	chr5:49447800-49451200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
7	chr5:49447800-49451200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
8	chr5:49448400-49451000	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:49448600-49450800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:49448600-49450800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
11	chr5:49448600-49451000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
12	chr5:49449200-49450000	Weak transcription	Brain Hippocampus Middle	brain
13	chr5:49449200-49450000	Weak transcription	HSMMtube	muscle
14	chr5:49449200-49450400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr5:49449200-49450400	Weak transcription	Liver	Liver
16	chr5:49449200-49450400	Weak transcription	Fetal Heart	heart
17	chr5:49449200-49450400	Weak transcription	Fetal Kidney	kidney
18	chr5:49449200-49450400	Weak transcription	Psoas Muscle	Psoas
19	chr5:49449200-49450400	Weak transcription	GM12878-XiMat	blood

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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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