Variant report

Variant	rs11161734
Chromosome Location	chr1:86569695-86569696
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10047143	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10873744	0.89[CEU][hapmap];0.86[TSI][hapmap]
rs11161713	0.89[TSI][hapmap]
rs12029694	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12043664	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs17405097	0.89[TSI][hapmap]
rs2390015	0.80[ASN][1000 genomes]
rs489385	0.81[EUR][1000 genomes]
rs498554	0.83[EUR][1000 genomes]
rs516213	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs535637	0.89[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs569419	0.89[CEU][hapmap]
rs582141	0.89[CEU][hapmap]
rs583315	0.89[CEU][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs610639	0.84[CEU][hapmap]
rs613060	0.89[CEU][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs61802174	0.83[EUR][1000 genomes]
rs61802177	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs640303	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs648833	0.81[EUR][1000 genomes]
rs662369	0.81[EUR][1000 genomes]
rs6665315	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6672107	1.00[CEU][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs997110	0.92[CEU][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs9988602	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	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
3	nsv1010312	chr1:86469730-86686426	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1012467	chr1:86494935-86686426	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1009092	chr1:86532988-86724805	Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv535024	chr1:86532988-86724805	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv830481	chr1:86550274-86737290	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11161734	LRRC8D	cis	cerebellum	SCAN
rs11161734	LOC339524	cis	parietal	SCAN
rs11161734	COL24A1	cis	Artery Tibial	GTEx
rs11161734	COL24A1	cis	lymphoblastoid	seeQTL
rs11161734	LOC339524	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86550800-86570400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:86556000-86570200	Weak transcription	Fetal Lung	lung
3	chr1:86569000-86570400	Weak transcription	H1 Cell Line	embryonic stem cell

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