Variant report

Variant	rs2483142
Chromosome Location	chr1:160947547-160947548
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12132502	0.82[EUR][1000 genomes]
rs2245672	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2246145	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2246484	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2246485	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2247472	0.80[EUR][1000 genomes]
rs2249409	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2249933	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2250174	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2250193	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2250304	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2256505	0.82[ASN][1000 genomes]
rs2256625	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2265239	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2265240	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2265242	0.82[AMR][1000 genomes]
rs2481073	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2481077	0.80[EUR][1000 genomes]
rs2483139	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2483140	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2779801	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2990694	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3007155	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4483427	0.89[ASN][1000 genomes]
rs6427563	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6427571	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6677526	0.84[EUR][1000 genomes]
rs6677533	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs790055	0.80[EUR][1000 genomes]
rs790056	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv548058	chr1:160925455-160989614	Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2483142	TSTD1	cis	Nerve Tibial	GTEx
rs2483142	F11R	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160943200-160951000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:160943200-160959800	Weak transcription	Pancreas	Pancrea
3	chr1:160943600-160949200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:160943800-160950600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:160944000-160950600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:160947000-160950600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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