Variant report

Variant	rs492054
Chromosome Location	chr1:93473744-93473745
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFYB	chr1:93473610-93473866	K562	blood:	n/a	n/a
2	ZNF143	chr1:93473725-93473846	H1-hESC	embryonic stem cell:	n/a	n/a
3	NFYB	chr1:93473634-93474362	GM12878	blood:	n/a	chr1:93474238-93474250 chr1:93474234-93474249 chr1:93474237-93474247 chr1:93474236-93474249 chr1:93474234-93474249 chr1:93474235-93474249 chr1:93474237-93474247

Variant related genes	Relation type
RNU6-210P	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11164860	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11164861	0.94[ASN][1000 genomes]
rs12022729	0.81[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs12023767	0.83[ASN][1000 genomes]
rs12027025	0.83[ASN][1000 genomes]
rs12039256	0.83[ASN][1000 genomes]
rs12043007	0.82[CHB][hapmap]
rs12043577	0.82[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs12119421	0.82[ASN][1000 genomes]
rs12130551	0.94[ASN][1000 genomes]
rs12134501	0.83[ASN][1000 genomes]
rs12141895	0.83[ASN][1000 genomes]
rs1678778	0.87[ASN][1000 genomes]
rs2086312	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2253595	0.85[ASN][1000 genomes]
rs2485032	0.85[EUR][1000 genomes]
rs2492898	0.82[ASN][1000 genomes]
rs2928183	0.96[ASN][1000 genomes]
rs4626900	0.83[ASN][1000 genomes]
rs481214	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4847227	0.88[ASN][1000 genomes]
rs485336	0.83[ASN][1000 genomes]
rs486370	0.87[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs492754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs496465	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs497540	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs504418	0.87[ASN][1000 genomes]
rs517856	0.81[ASN][1000 genomes]
rs521527	0.87[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs524045	0.84[ASN][1000 genomes]
rs553396	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs557812	0.86[ASN][1000 genomes]
rs56320266	0.94[ASN][1000 genomes]
rs572131	0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs57478994	0.84[ASN][1000 genomes]
rs590296	0.87[ASN][1000 genomes]
rs591820	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs591868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs592751	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs664524	0.85[ASN][1000 genomes]
rs664852	0.86[ASN][1000 genomes]
rs6674738	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs680285	0.83[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs681373	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs808833	0.83[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs9787147	0.85[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs492054	MTF2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93467000-93474600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:93471600-93478000	Weak transcription	GM12878-XiMat	blood
3	chr1:93473400-93474600	Enhancers	HSMM	muscle
4	chr1:93473600-93473800	Flanking Active TSS	NH-A	brain
5	chr1:93473600-93474000	Enhancers	H1 Cell Line	embryonic stem cell
6	chr1:93473600-93474000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:93473600-93474000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:93473600-93474000	Bivalent Enhancer	HepG2	liver
9	chr1:93473600-93474000	Enhancers	Osteobl	bone
10	chr1:93473600-93474200	Enhancers	HSMMtube	muscle
11	chr1:93473600-93474400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:93473600-93474400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr1:93473600-93474600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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