Variant report

Variant	rs11168618
Chromosome Location	chr12:48933233-48933234
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	chr12:48931723..48934359-chr12:48958892..48961149,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10875827	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875829	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10875833	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11168577	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168586	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168599	0.92[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168619	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168637	0.87[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11458	0.87[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12371700	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12425460	0.83[TSI][hapmap]
rs12815544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2114322	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2731091	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs2731094	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs2731102	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs35338015	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4359253	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57444623	0.88[ASN][1000 genomes]
rs6580671	0.92[CEU][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7302209	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7312017	0.94[JPT][hapmap];0.87[MEX][hapmap]
rs7955785	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7958521	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7972785	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7974213	0.85[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7976324	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7980421	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9268	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv1047600	chr12:48927514-48954225	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1048307	chr12:48927514-48958949	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Adiponectin levels	24105470	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11168618	ADAMTS20	cis	cerebellum	SCAN
rs11168618	CCNT1	cis	cerebellum	SCAN
rs11168618	RPAP3	cis	cerebellum	SCAN
rs11168618	OR10AD1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48932800-48934400	Enhancers	K562	blood
2	chr12:48933000-48933400	Enhancers	GM12878-XiMat	blood
3	chr12:48933000-48934800	Enhancers	Hela-S3	cervix

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