Variant report

Variant	rs6080109
Chromosome Location	chr20:16033620-16033621
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10485545	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12624898	0.86[AMR][1000 genomes]
rs1323300	0.86[AMR][1000 genomes]
rs16997016	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs16997071	0.80[AMR][1000 genomes]
rs16997087	0.86[AMR][1000 genomes]
rs2066089	0.83[AMR][1000 genomes]
rs6043705	0.95[ASN][1000 genomes]
rs6043708	0.94[ASN][1000 genomes]
rs6074997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6074998	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6074999	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6080103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6080104	1.00[ASW][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6080111	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62194240	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16029400-16033800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr20:16029600-16034200	Enhancers	Brain Germinal Matrix	brain
3	chr20:16031200-16039200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr20:16031800-16035000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr20:16031800-16035000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr20:16032200-16033800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr20:16032200-16033800	Enhancers	Brain Substantia Nigra	brain
8	chr20:16033000-16033800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr20:16033200-16045000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr20:16033400-16035000	Weak transcription	Primary B cells from cord blood	blood
11	chr20:16033600-16035000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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