Variant report

Variant	rs11808402
Chromosome Location	chr1:146501792-146501793
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10900384	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11240094	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11800992	0.83[ASN][1000 genomes]
rs11809158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122453	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12122534	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12139768	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12141387	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12142744	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12742988	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1925343	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1984615	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3862922	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4950330	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4950332	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6665804	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[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	nsv428224	chr1:145613243-146553918	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv2757753	chr1:145883119-146697542	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv872251	chr1:146152553-146803630	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
4	nsv946295	chr1:146471863-146507583	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv872252	chr1:146471863-147398135	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
6	nsv872253	chr1:146494246-146548549	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11808402	NBPF13P	cis	lung	GTEx
rs11808402	RP11-94I2.1	cis	lung	GTEx
rs11808402	RP11-325P15.1	cis	lung	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146494800-146504200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:146501000-146502600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:146501600-146501800	Enhancers	Muscle Satellite Cultured Cells	--
4	chr1:146501600-146506800	Weak transcription	NHEK	skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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