Variant report

Variant	rs17832389
Chromosome Location	chr14:56185836-56185837
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10083493	1.00[CHB][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs10083499	1.00[CHB][hapmap]
rs10133962	1.00[CHB][hapmap]
rs10137340	1.00[CHB][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs10137885	0.86[ASN][1000 genomes]
rs10139905	0.86[ASN][1000 genomes]
rs10142497	1.00[CHB][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs10142757	1.00[CHB][hapmap]
rs10143002	1.00[CHB][hapmap]
rs10150498	1.00[CHB][hapmap]
rs10483643	1.00[CHB][hapmap]
rs10483645	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10483646	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10483648	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10483650	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12100753	1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12100949	1.00[CHB][hapmap]
rs12886406	1.00[AFR][1000 genomes]
rs12892022	1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs12892413	1.00[AFR][1000 genomes]
rs12893081	1.00[AFR][1000 genomes]
rs12893836	1.00[AFR][1000 genomes]
rs12894368	1.00[CHB][hapmap]
rs17253716	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17253723	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17253744	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17253792	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17683614	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17683626	1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs17685078	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes]
rs17685102	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17745274	1.00[AFR][1000 genomes]
rs17745459	1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs17746033	1.00[CHB][hapmap]
rs17747083	1.00[CHB][hapmap]
rs17747301	1.00[CHB][hapmap]
rs17832365	1.00[CHB][hapmap]
rs17832371	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2147114	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2274075	1.00[CHB][hapmap]
rs2296181	1.00[CHB][hapmap]
rs28375514	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28537145	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28539882	0.86[ASN][1000 genomes]
rs28616134	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28661008	0.86[ASN][1000 genomes]
rs28663681	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34136598	1.00[AFR][1000 genomes]
rs34446601	1.00[AFR][1000 genomes]
rs35230683	1.00[AFR][1000 genomes]
rs35536987	1.00[AFR][1000 genomes]
rs3736876	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs45458197	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs45501402	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs71412688	1.00[AFR][1000 genomes]
rs71412689	1.00[AFR][1000 genomes]
rs71412690	1.00[AFR][1000 genomes]
rs71412693	1.00[AFR][1000 genomes]
rs71413577	1.00[AFR][1000 genomes]
rs71413578	1.00[AFR][1000 genomes]
rs7150841	1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs74051609	0.86[ASN][1000 genomes]
rs8006705	0.86[ASN][1000 genomes]
rs8007065	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs8008528	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs8009239	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs8010475	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8013714	0.86[ASN][1000 genomes]
rs8013831	0.86[ASN][1000 genomes]
rs9323289	1.00[CHB][hapmap]
rs9972177	1.00[CHB][hapmap]
rs9972178	1.00[CHB][hapmap]
rs9972180	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832804	chr14:56083850-56277632	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv901966	chr14:56160904-56436203	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv901967	chr14:56183127-56252062	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv901968	chr14:56183127-56256651	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv901969	chr14:56183127-56258997	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv901970	chr14:56183127-56265176	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv901971	chr14:56183127-56265176	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv901972	chr14:56185501-56256651	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17832389	KTN1	cis	brain	seeQTL
rs17832389	KTN1	trans	brain	seeQTL
rs17832389	KTN1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56154000-56191000	Weak transcription	Aorta	Aorta
2	chr14:56179800-56188800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr14:56179800-56189000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr14:56183400-56187600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr14:56183400-56187800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr14:56183400-56188000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr14:56185600-56189200	Weak transcription	HSMMtube	muscle
8	chr14:56185800-56187600	Weak transcription	Hela-S3	cervix

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