Variant report

Variant	rs13039811
Chromosome Location	chr20:31667742-31667743
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11696307	1.00[JPT][hapmap]
rs11696310	1.00[JPT][hapmap]
rs11696835	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11697605	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11699009	1.00[JPT][hapmap]
rs11699448	1.00[JPT][hapmap]
rs11700200	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13036385	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13036592	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13041016	0.83[ASW][hapmap];0.86[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13044139	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13044428	1.00[JPT][hapmap];0.83[MEX][hapmap]
rs13044703	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547004	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972201	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024934	1.00[JPT][hapmap]
rs2057261	1.00[JPT][hapmap]
rs2057262	1.00[JPT][hapmap]
rs2070323	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2070325	0.93[JPT][hapmap]
rs2070326	0.83[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[YRI][hapmap]
rs2070328	1.00[JPT][hapmap]
rs2073325	1.00[JPT][hapmap];0.83[MEX][hapmap]
rs221982	0.90[CHB][hapmap]
rs2424936	0.91[CHB][hapmap]
rs2424940	0.82[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs2424942	1.00[JPT][hapmap]
rs2424945	1.00[JPT][hapmap]
rs2424946	1.00[JPT][hapmap]
rs2424947	1.00[JPT][hapmap]
rs2424949	0.88[ASN][1000 genomes]
rs2424953	1.00[JPT][hapmap]
rs2424955	1.00[JPT][hapmap]
rs2889732	0.93[JPT][hapmap]
rs3926669	0.94[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4339026	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4911291	0.83[CHB][hapmap]
rs6057717	0.84[JPT][hapmap]
rs6059069	0.93[JPT][hapmap]
rs6059076	1.00[JPT][hapmap]
rs6059079	1.00[JPT][hapmap]
rs6088091	0.93[JPT][hapmap]
rs6141876	0.93[JPT][hapmap]
rs6141877	0.93[JPT][hapmap]
rs7265752	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs7267265	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs761933	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs761938	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1056411	chr20:31057037-31942835	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	esv2758519	chr20:31495807-31748166	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2758792	chr20:31495807-31748166	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13039811	DYNLRB1	cis	cerebellum	SCAN
rs13039811	KCNH7	trans	parietal	SCAN
rs13039811	GGT7	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:31657400-31670600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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