Variant report

Variant	rs3953095
Chromosome Location	chr1:160882789-160882790
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10797087	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10797089	0.84[EUR][1000 genomes]
rs10908809	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10908810	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10908811	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10908812	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10908813	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11265510	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11265514	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11265516	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11265519	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11587040	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12080285	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12125065	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12135639	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12740520	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1810924	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1855186	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1855187	0.88[EUR][1000 genomes]
rs1930596	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1930598	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2039415	0.81[EUR][1000 genomes]
rs2184064	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2225591	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2297559	0.81[EUR][1000 genomes]
rs34295669	0.88[EUR][1000 genomes]
rs3953093	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3953094	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4017453	0.88[EUR][1000 genomes]
rs4017455	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4129196	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656277	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4656282	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4656958	0.81[EUR][1000 genomes]
rs4656959	0.89[EUR][1000 genomes]
rs4656964	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6427552	0.83[AFR][1000 genomes]
rs6427559	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6658416	0.80[EUR][1000 genomes]
rs6674437	0.83[EUR][1000 genomes]
rs6691868	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6694415	0.87[EUR][1000 genomes]
rs6694743	0.82[EUR][1000 genomes]
rs6704490	0.87[EUR][1000 genomes]
rs7414826	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7551697	0.87[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	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	esv3430322	chr1:160851829-160920480	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv947200	chr1:160870136-160905390	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3953095	RP11-312J18.6	cis	Thyroid	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160880000-160884400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:160880600-160884000	Enhancers	Fetal Intestine Small	intestine
3	chr1:160881000-160882800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:160881000-160882800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr1:160882000-160883000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:160882000-160883200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:160882000-160883400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:160882000-160883800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:160882400-160882800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:160882400-160883600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:160882400-160883800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:160882600-160883800	Weak transcription	Fetal Intestine Large	intestine

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