Variant report

Variant	rs2092311
Chromosome Location	chr1:171281278-171281279
allele	C/G
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	CEBPB	chr1:171281270-171281678	MCF-7	breast:	n/a	chr1:171281492-171281503
2	CEBPB	chr1:171281256-171281580	MCF-7	breast:	n/a	chr1:171281492-171281503

Variant related genes	Relation type
FMO4	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10399602	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10399952	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798297	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes]
rs10912672	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10912673	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10912713	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912714	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912723	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10912736	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1126692	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11484641	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11484642	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11487396	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12057955	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12058402	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12059179	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12062692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068552	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12070766	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12072043	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12077231	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12077755	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079141	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12080449	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12081291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091482	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12092985	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094878	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12141555	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes]
rs12354390	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12726624	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12729885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12730181	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12742008	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12745080	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12747080	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12757839	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13376631	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16864302	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16864387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2006986	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2076322	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2284131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28741369	0.85[ASN][1000 genomes]
rs34118031	0.85[ASN][1000 genomes]
rs34320519	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4607925	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55949630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6424932	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6670639	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6674596	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs742350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs742351	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7512853	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519999	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541377	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2092311	FMO4	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171266600-171288400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:171276200-171282600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:171277600-171282600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr1:171280000-171283400	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr1:171280200-171282400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:171280200-171282600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:171280200-171282600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:171280200-171282600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:171280400-171282800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:171280400-171283200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:171280400-171283200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:171280600-171282800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:171280800-171283600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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