Variant report

Variant	rs11164869
Chromosome Location	chr1:93539212-93539213
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12062154	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs12080248	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12736775	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2391228	0.87[EUR][1000 genomes]
rs490153	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs546445	0.93[CEU][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs550892	0.93[CEU][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs566843	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6670960	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6696026	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6702666	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7555395	0.92[AMR][1000 genomes];0.89[EUR][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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv870775	chr1:93481640-93543119	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11164869	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs11164869	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs11164869	RP4-717I23.3	cis	Artery Aorta	GTEx
rs11164869	RP4-717I23.3	cis	lung	GTEx
rs11164869	CCDC18	Cis_1M	lymphoblastoid	RTeQTL
rs11164869	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs11164869	RP4-717I23.3	cis	Whole Blood	GTEx
rs11164869	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs11164869	RP4-717I23.3	cis	Artery Tibial	GTEx
rs11164869	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs11164869	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs11164869	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs11164869	RP4-717I23.3	cis	Thyroid	GTEx
rs11164869	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93538200-93543800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr1:93539200-93539400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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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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