Variant report

Variant	rs10512140
Chromosome Location	chr9:85997312-85997313
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	chr9:85996640..85999188-chr9:86152643..86154584,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172159	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10441792	0.87[MEX][hapmap]
rs10746703	0.83[CEU][hapmap]
rs10746705	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10780596	0.91[MEX][hapmap]
rs10780601	0.91[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10868000	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[MEX][hapmap];0.87[YRI][hapmap]
rs10868001	0.86[CHB][hapmap]
rs11140041	1.00[YRI][hapmap]
rs11140045	0.91[MEX][hapmap]
rs11140046	0.86[MEX][hapmap]
rs11140056	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11140065	0.86[GIH][hapmap]
rs12337675	0.83[GIH][hapmap]
rs12348065	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12350022	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12352281	0.85[YRI][hapmap]
rs13300839	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13439910	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1536889	0.82[CEU][hapmap];0.91[MEX][hapmap]
rs2375886	0.91[MEX][hapmap];1.00[YRI][hapmap]
rs34767126	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3860903	0.91[MEX][hapmap];1.00[YRI][hapmap]
rs3904188	0.88[GIH][hapmap]
rs3915916	0.91[MEX][hapmap];1.00[YRI][hapmap]
rs4242622	0.97[GIH][hapmap]
rs4877253	0.91[MEX][hapmap]
rs62560269	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7851145	1.00[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046491	chr9:85861492-86063992	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10512140	C9orf103	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85937400-85998000	Weak transcription	Aorta	Aorta
2	chr9:85958200-86007600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr9:85981000-85997800	Weak transcription	Left Ventricle	heart
4	chr9:85982600-85998800	Weak transcription	Ovary	ovary
5	chr9:85983000-85998400	Weak transcription	Fetal Brain Male	brain
6	chr9:85995400-85997800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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