Variant report

Variant	rs17489666
Chromosome Location	chr12:40502374-40502375
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr12:40501399-40502382	GM19099	blood:	n/a	n/a
2	ZNF384	chr12:40502130-40502468	GM12878	blood:	n/a	n/a
3	NFIC	chr12:40502003-40502456	GM12878	blood:	n/a	n/a
4	BHLHE40	chr12:40501287-40502380	GM12878	blood:	n/a	chr12:40502192-40502208
5	EBF1	chr12:40502212-40502398	GM12878	blood:	n/a	n/a
6	RUNX3	chr12:40501963-40502504	GM12878	blood:	n/a	chr12:40502288-40502303
7	RUNX3	chr12:40502050-40502478	GM12878	blood:	n/a	chr12:40502288-40502303

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40404217..40405558-chr12:40500388..40503110,15	MCF-7	breast:

Variant related genes	Relation type
SLC2A13	TF binding region

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs11564113	1.00[JPT][hapmap]
rs17442095	1.00[JPT][hapmap]
rs17442346	1.00[JPT][hapmap]
rs17442353	1.00[JPT][hapmap]
rs17442490	1.00[JPT][hapmap]
rs17442882	1.00[JPT][hapmap]
rs17443421	1.00[JPT][hapmap]
rs17443552	1.00[JPT][hapmap]
rs17458257	1.00[JPT][hapmap]
rs17458745	1.00[JPT][hapmap]
rs17458773	1.00[JPT][hapmap]
rs17458974	1.00[JPT][hapmap]
rs17460894	1.00[JPT][hapmap]
rs17460992	1.00[JPT][hapmap]
rs17465716	1.00[JPT][hapmap]
rs17465849	1.00[JPT][hapmap]
rs17465891	1.00[JPT][hapmap]
rs17466030	1.00[JPT][hapmap]
rs17483502	1.00[JPT][hapmap]
rs17489225	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489302	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489379	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489459	1.00[JPT][hapmap]
rs17489480	1.00[JPT][hapmap]
rs17489715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489889	1.00[AMR][1000 genomes]
rs17490013	1.00[JPT][hapmap]
rs17490418	1.00[AMR][1000 genomes]
rs17490578	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17490585	1.00[AMR][1000 genomes]
rs17490599	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17490620	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17490762	1.00[JPT][hapmap]
rs17491110	1.00[JPT][hapmap]
rs17518014	1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs17518050	1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518071	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518183	1.00[JPT][hapmap]
rs17518204	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518253	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518273	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518364	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518427	1.00[JPT][hapmap]
rs17518441	1.00[JPT][hapmap]
rs17518476	1.00[JPT][hapmap]
rs17518672	1.00[JPT][hapmap]
rs17518735	1.00[JPT][hapmap]
rs17518770	1.00[AMR][1000 genomes]
rs17518805	1.00[AMR][1000 genomes]
rs17518992	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17519566	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17519797	1.00[JPT][hapmap]
rs2708450	1.00[AMR][1000 genomes]
rs2708451	1.00[AMR][1000 genomes]
rs28365202	1.00[JPT][hapmap]
rs28370603	1.00[JPT][hapmap]
rs28370641	1.00[JPT][hapmap]
rs28370650	1.00[JPT][hapmap]
rs28370657	1.00[JPT][hapmap]
rs28370688	1.00[AMR][1000 genomes]
rs28370698	1.00[JPT][hapmap]
rs28370706	1.00[JPT][hapmap]
rs28370720	1.00[JPT][hapmap]
rs28370728	1.00[JPT][hapmap]
rs28370730	1.00[JPT][hapmap]
rs28370743	1.00[JPT][hapmap]
rs28370745	1.00[AMR][1000 genomes]
rs28370748	1.00[AMR][1000 genomes]
rs28370755	1.00[AMR][1000 genomes]
rs28370758	1.00[AMR][1000 genomes]
rs28370759	1.00[JPT][hapmap]
rs28370766	1.00[JPT][hapmap]
rs28370768	1.00[AMR][1000 genomes]
rs28370770	1.00[JPT][hapmap]
rs28370776	1.00[AMR][1000 genomes]
rs28370777	1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs28370778	1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs28370780	1.00[AMR][1000 genomes]
rs28370782	1.00[JPT][hapmap]
rs28370783	1.00[AMR][1000 genomes]
rs28370784	1.00[JPT][hapmap]
rs28370786	1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs28370792	1.00[JPT][hapmap]
rs28370801	1.00[JPT][hapmap]
rs28370811	1.00[JPT][hapmap]
rs28370825	1.00[JPT][hapmap]
rs7306747	1.00[AMR][1000 genomes]
rs7307258	1.00[AMR][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	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	nsv899028	chr12:40478652-40524180	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	esv1846566	chr12:40498683-40527395	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	esv1838306	chr12:40499495-40527395	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40501200-40502800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:40501200-40510200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:40501600-40502400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:40501600-40502600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:40501600-40504200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:40501600-40504400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:40501600-40504400	Weak transcription	NHDF-Ad	bronchial
8	chr12:40502200-40502400	Flanking Active TSS	GM12878-XiMat	blood
9	chr12:40502200-40502600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:40502200-40503200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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