Variant report

Variant	rs17121868
Chromosome Location	chr12:59418718-59418719
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11172836	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11609012	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611254	0.82[CEU][hapmap];1.00[TSI][hapmap]
rs11833888	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17121746	0.82[CEU][hapmap]
rs17121834	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17121856	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17121860	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17121863	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17121866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17121873	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17121944	0.80[AFR][1000 genomes]
rs1823337	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59340973	1.00[ASN][1000 genomes]
rs73354920	1.00[ASN][1000 genomes]
rs73354921	1.00[ASN][1000 genomes]
rs73354927	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73354930	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73354933	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73354934	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73354937	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73354942	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	nsv526485	chr12:59412802-59422668	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	n/a
7	nsv522058	chr12:59416727-59422668	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17121868	CHI3L2	trans	brain	seeQTL

Chromatin state (count:5 , 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
2	chr12:59416000-59418800	Weak transcription	Aorta	Aorta
3	chr12:59417200-59418800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:59417400-59419200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr12:59417600-59430200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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