Variant report

Variant	rs11140298
Chromosome Location	chr9:86542206-86542207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86536152..86538297-chr9:86540828..86543846,3	MCF-7	breast:
2	chr9:86541635..86544345-chr9:86665548..86667347,2	K562	blood:
3	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: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10868069	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10868072	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11140284	0.82[EUR][1000 genomes]
rs12001293	0.87[GIH][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs12001918	0.88[CEU][hapmap];0.95[GIH][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs12003101	0.88[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12552069	0.88[CEU][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs17064724	0.88[CEU][hapmap];0.95[GIH][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap]
rs17086750	0.87[GIH][hapmap];0.92[TSI][hapmap]
rs2184086	0.88[CEU][hapmap];0.91[GIH][hapmap];0.85[LWK][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs34690696	0.81[EUR][1000 genomes]
rs4480186	0.88[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55872219	0.82[EUR][1000 genomes]
rs58474042	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7021609	0.88[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs7027121	0.88[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs7045525	0.82[CEU][hapmap];0.82[YRI][hapmap]
rs7046229	0.81[EUR][1000 genomes]
rs7048626	0.88[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs73463379	0.83[EUR][1000 genomes]
rs73463395	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73469343	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7850640	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7853625	0.83[CEU][hapmap];0.88[YRI][hapmap]
rs7854432	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7856614	0.88[CEU][hapmap];0.82[YRI][hapmap]
rs7857619	0.82[CEU][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs7859830	0.83[EUR][1000 genomes]
rs7867221	0.88[CEU][hapmap];0.82[YRI][hapmap]
rs7874481	0.88[CEU][hapmap];0.95[GIH][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap]
rs9695726	0.86[EUR][1000 genomes]
rs970846	0.88[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv438108	chr9:86488586-86542206	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
7	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
8	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
rs11140298	C4orf31	trans	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 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	chr9:86537800-86542600	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr9:86542000-86546400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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