Variant report

Variant	rs58474042
Chromosome Location	chr9:86543420-86543421
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86543303..86546156-chr9:86594809..86597216,2	K562	blood:
2	chr9:86536152..86538297-chr9:86540828..86543846,3	MCF-7	breast:
3	chr9:86541635..86544345-chr9:86665548..86667347,2	K562	blood:
4	chr9:86542024..86543859-chr9:86595135..86597329,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165119	Chromatin interaction
ENSG00000178966	Chromatin interaction
ENSG00000165115	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10868072	0.84[EUR][1000 genomes]
rs11140298	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12001293	0.85[EUR][1000 genomes]
rs12001505	0.90[EUR][1000 genomes]
rs12001918	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12003101	0.93[EUR][1000 genomes]
rs12003500	0.90[EUR][1000 genomes]
rs12552069	0.87[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs17086750	0.91[EUR][1000 genomes]
rs2184086	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs34690696	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs35784768	0.92[EUR][1000 genomes]
rs4480186	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55654273	0.81[EUR][1000 genomes]
rs55872219	0.98[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs56055736	0.98[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs57267691	0.90[EUR][1000 genomes]
rs57531526	0.84[EUR][1000 genomes]
rs57957686	0.88[EUR][1000 genomes]
rs58248061	0.88[EUR][1000 genomes]
rs60277614	0.90[EUR][1000 genomes]
rs61490202	0.88[EUR][1000 genomes]
rs7038235	0.92[EUR][1000 genomes]
rs7040843	0.88[EUR][1000 genomes]
rs7041687	0.80[EUR][1000 genomes]
rs7042053	0.80[EUR][1000 genomes]
rs7046229	0.94[EUR][1000 genomes]
rs7048626	0.88[EUR][1000 genomes]
rs73463313	0.81[EUR][1000 genomes]
rs73463327	0.88[EUR][1000 genomes]
rs73463379	0.98[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs73463395	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73469343	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7849708	0.86[EUR][1000 genomes]
rs7850288	0.88[EUR][1000 genomes]
rs7850404	0.88[EUR][1000 genomes]
rs7850640	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7854432	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7857619	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7859830	0.98[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7859928	0.86[EUR][1000 genomes]
rs7874481	0.92[EUR][1000 genomes]
rs970846	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469859	chr9:86398152-86587957	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv482641	chr9:86398152-86587957	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS 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	85 gene(s)	inside rSNPs	diseases
5	nsv8541	chr9:86469723-86593758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
7	esv3366490	chr9:86541369-86608868	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58474042	C4orf31	trans	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86536600-86571000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:86537000-86543800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:86537000-86553600	Weak transcription	Fetal Intestine Small	intestine
4	chr9:86537000-86553600	Weak transcription	Thymus	Thymus
5	chr9:86537200-86545600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr9:86542000-86546400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr9:86543000-86545400	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr9:86543000-86547000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr9:86543000-86571000	Weak transcription	Esophagus	oesophagus
10	chr9:86543400-86543600	Enhancers	Lung	lung

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