Variant report

Variant	rs6692784
Chromosome Location	chr1:86794839-86794840
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10489735	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493789	0.89[CHB][hapmap]
rs10747328	0.88[ASW][hapmap];0.89[CHB][hapmap];0.80[CHD][hapmap]
rs10873777	0.83[ASW][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap]
rs1158505	0.89[CHB][hapmap]
rs11808143	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1182102	0.83[ASW][hapmap];0.87[MEX][hapmap]
rs12741520	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12755828	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323027	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1323029	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1323030	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1323031	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1323034	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1334140	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1334143	0.84[CHB][hapmap]
rs1334148	0.84[CHB][hapmap]
rs1575413	0.99[ASN][1000 genomes]
rs1575414	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1575415	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17129055	0.87[ASN][1000 genomes]
rs175363	0.83[ASW][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.85[MEX][hapmap]
rs185655	0.84[CHB][hapmap]
rs1931363	0.89[CHB][hapmap]
rs2181419	0.99[ASN][1000 genomes]
rs2208925	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2390100	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs272491	0.89[CHB][hapmap]
rs272492	0.84[CHB][hapmap];0.83[GIH][hapmap]
rs272498	0.87[CHB][hapmap]
rs272504	0.83[ASW][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap]
rs272507	0.83[ASW][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap]
rs272516	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs34747640	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765975	0.89[CHB][hapmap];0.82[CHD][hapmap]
rs410807	1.00[ASN][1000 genomes]
rs450927	1.00[ASN][1000 genomes]
rs452865	1.00[ASN][1000 genomes]
rs567133	0.98[ASN][1000 genomes]
rs569912	1.00[ASN][1000 genomes]
rs61800656	0.87[ASN][1000 genomes]
rs6660770	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6673014	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6685789	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6689064	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6695671	0.89[CHB][hapmap]
rs6701074	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6704104	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7527383	1.00[ASN][1000 genomes]
rs7527390	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533682	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7536173	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7542133	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548881	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs768610	0.99[ASN][1000 genomes]
rs9787365	0.87[ASN][1000 genomes]
rs990771	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871866	chr1:86726619-86851420	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6692784	SEP15	cis	parietal	SCAN
rs6692784	ODF2L	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86791400-86804600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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