Variant report

Variant	rs241554
Chromosome Location	chr14:56549166-56549167
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10140006	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1041075	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1046596	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10873093	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs171339	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2010895	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs241513	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs241514	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs241521	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs241522	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241549	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs241551	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241552	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241556	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241558	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241561	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs241562	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs241564	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs241565	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3186565	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs377471	0.82[JPT][hapmap]
rs3850294	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3850295	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs387419	0.83[MEX][hapmap]
rs4901637	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61526546	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7149660	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7150067	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7156007	0.81[EUR][1000 genomes]
rs7157298	0.81[EUR][1000 genomes]
rs8004543	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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	esv34106	chr14:56346245-56550642	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs241554	TMX1	cis	cerebellum	SCAN
rs241554	FBXO34	cis	cerebellum	SCAN
rs241554	PELI2	cis	parietal	SCAN
rs241554	C14orf166	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56541000-56554200	Weak transcription	Gastric	stomach
2	chr14:56547800-56550400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr14:56548400-56549600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr14:56548600-56550000	Enhancers	Fetal Intestine Small	intestine
5	chr14:56549000-56549200	Enhancers	H9 Cell Line	embryonic stem cell
6	chr14:56549000-56549400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr14:56549000-56549400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr14:56549000-56549400	Enhancers	Dnd41	blood

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