Variant report

Variant	rs16939940
Chromosome Location	chr18:44250315-44250316
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1073745	0.80[ASN][1000 genomes]
rs11665368	0.82[LWK][hapmap]
rs11872518	0.86[CHB][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs11872859	1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11873719	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12953964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12953965	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960373	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34198703	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3809956	0.80[ASN][1000 genomes]
rs3826589	0.80[ASN][1000 genomes]
rs71364554	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71364555	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72915489	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs948569	0.82[CEU][hapmap]
rs948570	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428355	chr18:44160181-44406285	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	esv15009	chr18:44222960-44263857	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv515609	chr18:44223365-44263237	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1056493	chr18:44224972-44259409	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1064019	chr18:44224972-44263237	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1065369	chr18:44224972-44263913	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1058904	chr18:44224972-44264578	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1060496	chr18:44229485-44263237	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16939940	ST8SIA5	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44248200-44252000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr18:44248200-44252400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr18:44248200-44256400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr18:44248200-44256400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr18:44248400-44253800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr18:44248600-44252200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr18:44248600-44252600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr18:44248600-44258800	Weak transcription	Brain Germinal Matrix	brain
9	chr18:44249200-44253800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr18:44249400-44253800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr18:44249600-44252000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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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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