Variant report

Variant	rs17489889
Chromosome Location	chr12:40531872-40531873
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40526853..40529105-chr12:40530805..40532717,2	MCF-7	breast:
2	12:40525880-40532672..12:40703633-40711447	GM12878	blood:

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs17489225	1.00[AMR][1000 genomes]
rs17489302	1.00[AMR][1000 genomes]
rs17489379	1.00[AMR][1000 genomes]
rs17489666	1.00[AMR][1000 genomes]
rs17489715	1.00[AMR][1000 genomes]
rs17489722	1.00[AMR][1000 genomes]
rs17490418	1.00[AMR][1000 genomes]
rs17490578	1.00[AMR][1000 genomes]
rs17490585	1.00[AMR][1000 genomes]
rs17490599	1.00[AMR][1000 genomes]
rs17490620	1.00[AMR][1000 genomes]
rs17518014	1.00[AMR][1000 genomes]
rs17518050	1.00[AMR][1000 genomes]
rs17518071	1.00[AMR][1000 genomes]
rs17518204	1.00[AMR][1000 genomes]
rs17518253	1.00[AMR][1000 genomes]
rs17518273	1.00[AMR][1000 genomes]
rs17518364	1.00[AMR][1000 genomes]
rs17518770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518992	1.00[AMR][1000 genomes]
rs17519566	1.00[AMR][1000 genomes]
rs2708450	1.00[AMR][1000 genomes]
rs2708451	1.00[AMR][1000 genomes]
rs28370688	1.00[AMR][1000 genomes]
rs28370745	1.00[AMR][1000 genomes]
rs28370748	1.00[AMR][1000 genomes]
rs28370755	1.00[AMR][1000 genomes]
rs28370758	1.00[AMR][1000 genomes]
rs28370768	1.00[AMR][1000 genomes]
rs28370776	1.00[AMR][1000 genomes]
rs28370777	1.00[AMR][1000 genomes]
rs28370778	1.00[AMR][1000 genomes]
rs28370780	1.00[AMR][1000 genomes]
rs28370783	1.00[AMR][1000 genomes]
rs28370786	1.00[AMR][1000 genomes]
rs7306747	1.00[AMR][1000 genomes]
rs7307258	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv899029	chr12:40478652-40536061	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv1836585	chr12:40492814-40540939	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv1839483	chr12:40492814-40540939	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv899030	chr12:40509341-40580440	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv899031	chr12:40520684-40580440	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40530800-40532000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr12:40531200-40532000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr12:40531200-40532400	Enhancers	HMEC	breast
4	chr12:40531400-40532600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:40531400-40532600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:40531400-40532600	Enhancers	NHEK	skin
7	chr12:40531600-40532800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:40531800-40532800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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