Variant report

Variant	rs2011345
Chromosome Location	chr1:171322521-171322522
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171289560..171292319-chr1:171321362..171324920,3	K562	blood:

Variant related genes	Relation type
ENSG00000076258	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10157634	0.93[ASN][1000 genomes]
rs1018390	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1018392	0.81[ASN][1000 genomes]
rs1024171	0.93[ASN][1000 genomes]
rs1024173	0.96[ASN][1000 genomes]
rs1042772	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10912810	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs10912830	0.96[ASN][1000 genomes]
rs10912833	0.92[ASN][1000 genomes]
rs10912842	0.85[ASN][1000 genomes]
rs11807475	0.87[ASN][1000 genomes]
rs12057885	0.93[ASN][1000 genomes]
rs12064618	0.96[ASN][1000 genomes]
rs12121479	0.90[ASN][1000 genomes]
rs12406999	0.90[CHB][hapmap]
rs12564530	0.92[ASN][1000 genomes]
rs12735239	0.93[ASN][1000 genomes]
rs12736204	0.93[ASN][1000 genomes]
rs12737633	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs12747017	0.93[ASN][1000 genomes]
rs1963273	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2011548	0.93[ASN][1000 genomes]
rs2143090	0.93[ASN][1000 genomes]
rs2179375	0.93[ASN][1000 genomes]
rs2223477	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2235508	0.90[ASN][1000 genomes]
rs2235509	0.90[ASN][1000 genomes]
rs2235510	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2235511	0.90[ASN][1000 genomes]
rs34668298	0.90[ASN][1000 genomes]
rs35062585	0.93[ASN][1000 genomes]
rs36112567	0.90[ASN][1000 genomes]
rs4615872	0.93[ASN][1000 genomes]
rs6425167	0.84[ASN][1000 genomes]
rs6425192	0.94[ASN][1000 genomes]
rs6425194	0.94[ASN][1000 genomes]
rs6656117	0.96[ASN][1000 genomes]
rs6656219	0.96[ASN][1000 genomes]
rs6662297	0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs6667507	0.92[ASN][1000 genomes]
rs6670432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670627	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs6688317	0.93[ASN][1000 genomes]
rs6699676	0.89[ASN][1000 genomes]
rs67595287	0.93[ASN][1000 genomes]
rs71573031	0.84[ASN][1000 genomes]
rs7515001	0.90[CHB][hapmap];0.88[CHD][hapmap]
rs7516677	0.90[ASN][1000 genomes]
rs7518648	0.90[ASN][1000 genomes]
rs7519001	0.93[ASN][1000 genomes]
rs7548166	0.93[ASN][1000 genomes]
rs7555359	0.90[ASN][1000 genomes]
rs980120	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv1002423	chr1:171294384-171376936	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv548188	chr1:171308832-171371998	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2011345	FMO4	cis	Artery Tibial	GTEx
rs2011345	KIAA1958	trans	cerebellum	SCAN
rs2011345	FMO4	cis	parietal	SCAN
rs2011345	BRP44	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171315400-171324800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:171322000-171325400	Weak transcription	Liver	Liver
3	chr1:171322200-171322600	Enhancers	H1 Cell Line	embryonic stem cell
4	chr1:171322200-171325000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:171322400-171322600	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr1:171322400-171322800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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