Variant report

Variant	rs16997056
Chromosome Location	chr20:16043408-16043409
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1033858	0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10485543	1.00[ASN][1000 genomes]
rs17644136	1.00[ASN][1000 genomes]
rs17646021	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs41309829	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57792062	1.00[ASN][1000 genomes]
rs6034367	1.00[ASN][1000 genomes]
rs6043703	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6043706	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60854916	1.00[ASN][1000 genomes]
rs6105508	1.00[ASN][1000 genomes]
rs7271371	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73092725	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73092737	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73095217	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237726	1.00[ASN][1000 genomes]
rs73237730	1.00[ASN][1000 genomes]
rs8116533	0.85[YRI][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8122540	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs912184	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs912186	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[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	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	nsv585649	chr20:16004320-16066764	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16997056	SLC24A3	cis	cerebellum	SCAN
rs16997056	C20orf72	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16033200-16045000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr20:16039400-16044400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr20:16039600-16043600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr20:16039600-16045200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr20:16040000-16043600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr20:16040600-16045200	Weak transcription	Adipose Nuclei	Adipose
7	chr20:16042000-16047000	Enhancers	Brain Germinal Matrix	brain
8	chr20:16042400-16044000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr20:16042400-16044000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr20:16042400-16045000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr20:16042600-16043800	Weak transcription	Fetal Stomach	stomach
12	chr20:16043200-16043600	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr20:16043200-16045000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr20:16043200-16045600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr20:16043400-16044000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr20:16043400-16045200	Weak transcription	Fetal Heart	heart
17	chr20:16043400-16046600	Enhancers	HSMM	muscle
18	chr20:16043400-16048000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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