Variant report

Variant	rs16996681
Chromosome Location	chr20:15830144-15830145
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12480694	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12481296	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16996627	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2041420	0.82[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs2191518	0.93[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs2327968	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[ASN][1000 genomes]
rs2876414	0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[ASN][1000 genomes]
rs34591655	0.84[AMR][1000 genomes]
rs4555415	0.88[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs4814404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4814405	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4814406	0.87[CHB][hapmap];0.80[JPT][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6034299	0.88[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs6034302	0.86[ASN][1000 genomes]
rs6043561	0.90[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs6043570	0.88[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs6079982	0.84[ASN][1000 genomes]
rs6079983	0.87[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs6131728	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6131729	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6131731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6131733	1.00[ASW][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6135567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6135568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6135569	0.82[EUR][1000 genomes]
rs6135570	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6135571	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6135572	0.89[EUR][1000 genomes]
rs6135574	0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7268461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs978767	0.82[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs978768	0.82[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv833929	chr20:15765372-15977337	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:15829200-15830200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr20:15829400-15830200	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr20:15829400-15830200	Enhancers	Brain Substantia Nigra	brain
4	chr20:15829600-15830200	Enhancers	H1 Cell Line	embryonic stem cell
5	chr20:15829600-15830200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr20:15829600-15830200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:15829600-15830200	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr20:15829600-15830200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr20:15829600-15830200	Flanking Active TSS	Brain Anterior Caudate	brain
10	chr20:15829600-15830200	Flanking Active TSS	Brain Cingulate Gyrus	brain
11	chr20:15829600-15830200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr20:15829800-15830200	Flanking Active TSS	Brain Angular Gyrus	brain
13	chr20:15829800-15830200	Flanking Active TSS	Brain Germinal Matrix	brain
14	chr20:15829800-15830200	Flanking Active TSS	Brain Hippocampus Middle	brain
15	chr20:15829800-15830200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
16	chr20:15829800-15830400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr20:15829800-15830400	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr20:15829800-15830400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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