Variant report

Variant	rs1885941
Chromosome Location	chr20:16096330-16096331
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs13044905	0.83[ASN][1000 genomes]
rs1359065	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1923951	0.90[AFR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1923952	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010736	0.83[ASN][1000 genomes]
rs2224734	0.90[AFR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2476314	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2476315	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2760543	0.83[ASN][1000 genomes]
rs2760545	0.90[EUR][1000 genomes]
rs2760546	0.90[EUR][1000 genomes]
rs2760547	0.89[EUR][1000 genomes]
rs2760549	0.88[EUR][1000 genomes]
rs2760557	0.88[EUR][1000 genomes]
rs2788928	0.88[EUR][1000 genomes]
rs2788929	0.86[EUR][1000 genomes]
rs4814438	0.82[EUR][1000 genomes]
rs6110906	0.90[AFR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs753665	0.91[EUR][1000 genomes]
rs8114116	0.90[AFR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8114154	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869328	chr20:15325423-16213898	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3447866	chr20:15799286-16115291	Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1059778	chr20:15999519-16165895	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv544207	chr20:15999519-16165895	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1061301	chr20:16007489-16097070	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	esv3424095	chr20:16094018-16103817	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	n/a
7	esv3439085	chr20:16094028-16103826	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1885941	ESF1	cis	parietal	SCAN
rs1885941	STARD10	trans	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16088400-16106000	Weak transcription	Psoas Muscle	Psoas
2	chr20:16089000-16096600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr20:16093200-16096400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr20:16096000-16096400	Weak transcription	Left Ventricle	heart
5	chr20:16096200-16096400	Flanking Active TSS	Fetal Heart	heart
6	chr20:16096200-16096800	Enhancers	Fetal Brain Male	brain
7	chr20:16096200-16097200	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr20:16096200-16097200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr20:16096200-16097400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr20:16096200-16098000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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