Variant report

Variant	rs11172869
Chromosome Location	chr12:59412220-59412221
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	chr12:59411769..59412269-chr7:158497029..158497610,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000146918	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10877198	0.82[EUR][1000 genomes]
rs10877200	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172823	0.83[TSI][hapmap]
rs11172824	0.83[TSI][hapmap]
rs11172837	0.84[EUR][1000 genomes]
rs11172839	0.84[EUR][1000 genomes]
rs11172840	0.84[EUR][1000 genomes]
rs11172846	0.84[EUR][1000 genomes]
rs11172857	0.84[EUR][1000 genomes]
rs11172858	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172860	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172861	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172862	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172866	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172867	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172868	0.82[EUR][1000 genomes]
rs11172870	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172873	0.95[ASN][1000 genomes]
rs11172874	1.00[ASN][1000 genomes]
rs11172876	0.86[ASN][1000 genomes]
rs11172878	0.86[ASN][1000 genomes]
rs11172880	0.86[ASN][1000 genomes]
rs11172898	0.86[ASN][1000 genomes]
rs12367126	0.95[ASN][1000 genomes]
rs12368752	0.84[EUR][1000 genomes]
rs12369750	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1444099	0.86[ASN][1000 genomes]
rs1444102	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1568303	0.86[ASN][1000 genomes]
rs17121828	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17121844	0.84[AFR][1000 genomes]
rs17121848	0.92[AFR][1000 genomes]
rs17121854	0.91[AFR][1000 genomes]
rs17536893	0.95[ASN][1000 genomes]
rs55888651	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57205785	0.95[ASN][1000 genomes]
rs58692617	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60522760	0.84[EUR][1000 genomes]
rs61919469	0.84[EUR][1000 genomes]
rs61919471	0.82[EUR][1000 genomes]
rs61919513	0.84[EUR][1000 genomes]
rs61919518	0.84[EUR][1000 genomes]
rs61919519	0.84[EUR][1000 genomes]
rs61919520	0.82[EUR][1000 genomes]
rs61919521	0.84[EUR][1000 genomes]
rs61919523	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61919524	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61919525	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61919531	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61919532	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581224	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7136193	0.81[GIH][hapmap];0.91[TSI][hapmap]
rs7138401	0.84[EUR][1000 genomes]
rs7301299	0.84[EUR][1000 genomes]
rs7302365	0.84[EUR][1000 genomes]
rs7303773	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7309872	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs74091469	0.92[AFR][1000 genomes]
rs74091470	0.92[AFR][1000 genomes]
rs7960109	0.95[ASN][1000 genomes]
rs7963207	0.84[EUR][1000 genomes]
rs7968111	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7974440	0.82[EUR][1000 genomes]
rs7980955	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv559048	chr12:59336737-59440659	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv559049	chr12:59359937-59436179	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	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
rs11172869	RAB5B	cis	cerebellum	SCAN
rs11172869	MBD6	cis	cerebellum	SCAN
rs11172869	PIP4K2C	cis	cerebellum	SCAN
rs11172869	COQ10A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59408600-59420800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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