Variant report

Variant	rs3816953
Chromosome Location	chr1:213093636-213093637
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10864028	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10864029	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11120067	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11576311	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11582817	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11586314	0.84[AMR][1000 genomes]
rs11586464	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12140722	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12140754	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184323	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1284863	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3816952	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816956	0.99[ASN][1000 genomes]
rs3816957	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4951474	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4951655	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656128	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6656232	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6670064	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6679848	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679938	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679951	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7523310	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7523329	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7533476	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7533575	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs870547	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs871767	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008383	chr1:213025546-213114894	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs3816953	FLVCR1-AS1	cis	Stomach	GTEx
rs3816953	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs3816953	NSL1	Cis_1M	lymphoblastoid	RTeQTL
rs3816953	FLVCR1-AS1	cis	Esophagus Mucosa	GTEx
rs3816953	FLVCR1-AS1	cis	Thyroid	GTEx
rs3816953	VASH2	Cis_1M	lymphoblastoid	RTeQTL
rs3816953	FLVCR1-AS1	cis	Whole Blood	GTEx
rs3816953	FLVCR1-AS1	cis	Nerve Tibial	GTEx
rs3816953	FLVCR1-AS1	cis	lung	GTEx
rs3816953	FLVCR1-AS1	cis	Artery Aorta	GTEx
rs3816953	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs3816953	FLVCR1	cis	multi-tissue	Pritchard
rs3816953	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs3816953	FLVCR1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs3816953	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs3816953	FLVCR1-AS1	cis	Muscle Skeletal	GTEx
rs3816953	FLVCR1-AS1	cis	Artery Tibial	GTEx
rs3816953	FLVCR1-AS1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213086800-213094400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:213090600-213101800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:213090800-213101200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr1:213090800-213101200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:213090800-213101200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:213091200-213095000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:213091800-213100400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:213092200-213098600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:213092200-213101400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:213092600-213098200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:213092800-213101200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:213093000-213098000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:213093600-213094000	Flanking Active TSS	GM12878-XiMat	blood

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