Variant report

Variant	rs11120044
Chromosome Location	chr1:213022702-213022703
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10779588	0.84[AMR][1000 genomes]
rs10864010	0.84[AMR][1000 genomes]
rs10864028	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10864029	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11120042	0.82[AMR][1000 genomes]
rs11120049	0.84[AMR][1000 genomes]
rs11582817	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11586464	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12023052	0.84[AMR][1000 genomes]
rs12140831	0.84[AMR][1000 genomes]
rs2201601	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279692	0.85[AMR][1000 genomes]
rs6670064	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs963328	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv508691	chr1:212998319-213028392	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
3	nsv1011186	chr1:213005165-213069563	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1013705	chr1:213005344-213064209	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	esv3413107	chr1:213021779-213025977	Weak transcription ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs11120044	FLVCR1-AS1	cis	Artery Tibial	GTEx
rs11120044	FLVCR1-AS1	cis	Thyroid	GTEx
rs11120044	FLVCR1-AS1	cis	Heart Left Ventricle	GTEx
rs11120044	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs11120044	FLVCR1-AS1	cis	Esophagus Mucosa	GTEx
rs11120044	FLVCR1-AS1	cis	lung	GTEx
rs11120044	VASH2	Cis_1M	lymphoblastoid	RTeQTL
rs11120044	FLVCR1-AS1	cis	Whole Blood	GTEx
rs11120044	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs11120044	FLVCR1	cis	multi-tissue	Pritchard
rs11120044	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs11120044	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs11120044	FLVCR1-AS1	cis	Muscle Skeletal	GTEx
rs11120044	FLVCR1-AS1	cis	Artery Aorta	GTEx
rs11120044	FLVCR1-AS1	cis	Stomach	GTEx
rs11120044	NSL1	Cis_1M	lymphoblastoid	RTeQTL
rs11120044	FLVCR1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs11120044	FLVCR1-AS1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213020400-213028600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:213021600-213026800	Weak transcription	HepG2	liver
3	chr1:213022600-213030000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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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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