Variant report

Variant	rs12790020
Chromosome Location	chr11:9017984-9017985
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	chr11:8992414..8994914-chr11:9017191..9020958,3	K562	blood:
2	chr11:9016089..9018406-chr11:9024476..9026148,2	K562	blood:

Variant related genes	Relation type
ENSG00000175352	Chromatin interaction
ENSG00000253973	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10219366	0.82[EUR][1000 genomes]
rs10769976	0.83[EUR][1000 genomes]
rs10840156	0.83[EUR][1000 genomes]
rs12785559	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12786377	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12794962	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12805109	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1347016	0.87[ASN][1000 genomes]
rs1985026	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016844	0.80[EUR][1000 genomes]
rs2056903	0.80[EUR][1000 genomes]
rs2116510	0.87[ASN][1000 genomes]
rs2116511	0.87[ASN][1000 genomes]
rs2246878	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2247038	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2252102	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2316541	0.85[ASN][1000 genomes]
rs2568047	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568069	0.87[ASN][1000 genomes]
rs2568074	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2568075	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2568077	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2568079	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2568081	0.85[ASN][1000 genomes]
rs2568086	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2568087	0.87[ASN][1000 genomes]
rs2568088	0.81[ASN][1000 genomes]
rs2653590	0.87[ASN][1000 genomes]
rs2653601	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2653604	0.87[ASN][1000 genomes]
rs2653611	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2742473	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742486	0.87[ASN][1000 genomes]
rs2742487	0.87[ASN][1000 genomes]
rs2742488	0.87[ASN][1000 genomes]
rs2742489	0.81[ASN][1000 genomes]
rs2742491	0.87[ASN][1000 genomes]
rs2742493	0.87[ASN][1000 genomes]
rs2742495	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2742496	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2742497	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2742504	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2742505	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2742512	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2742513	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2742514	0.81[ASN][1000 genomes]
rs3751063	0.83[EUR][1000 genomes]
rs4264185	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4370967	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4909951	0.83[EUR][1000 genomes]
rs4910313	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66630602	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7124403	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72852790	0.85[ASN][1000 genomes]
rs72853712	0.85[ASN][1000 genomes]
rs7940895	0.87[ASN][1000 genomes]
rs909464	0.80[EUR][1000 genomes]
rs9300096	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv896984	chr11:8988550-9090408	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv896985	chr11:9013002-9152463	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12790020	C11orf17	Cis_1M	lymphoblastoid	RTeQTL
rs12790020	C11orf17	cis	multi-tissue	Pritchard

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8989600-9019600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:9011000-9023200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:9011800-9023000	Weak transcription	NHDF-Ad	bronchial
4	chr11:9016000-9019400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:9017800-9019600	Weak transcription	K562	blood

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