Variant report

Variant	rs17745274
Chromosome Location	chr14:55997881-55997882
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	chr14:55995958..55999191-chr14:56000283..56002949,4	MCF-7	breast:

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10083303	0.81[AMR][1000 genomes]
rs10083353	0.81[AMR][1000 genomes]
rs10083493	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10083499	1.00[CHB][hapmap]
rs10133962	1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs10136155	0.81[AMR][1000 genomes]
rs10137340	1.00[CHB][hapmap]
rs10142497	1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs10142757	1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs10143002	1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs10146604	0.87[ASN][1000 genomes]
rs10148983	0.81[AMR][1000 genomes]
rs10149408	0.87[ASN][1000 genomes]
rs10150498	1.00[CHB][hapmap]
rs10483643	1.00[CHB][hapmap]
rs10483645	1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs10483646	1.00[AFR][1000 genomes]
rs10483648	1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs10483650	1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs12100753	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs12100949	1.00[CHB][hapmap]
rs12879564	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12879705	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12880362	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12883972	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12886406	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12893061	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12893610	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12893676	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12894368	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12894613	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379342	0.81[AMR][1000 genomes]
rs13379343	0.81[AMR][1000 genomes]
rs17253716	1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs17253723	1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs17253744	1.00[AFR][1000 genomes]
rs17683614	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17683626	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17683656	0.81[AMR][1000 genomes]
rs17683728	0.81[AMR][1000 genomes]
rs17685078	1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs17685102	1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs17744929	1.00[AFR][1000 genomes]
rs17745459	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17746033	1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs17747083	1.00[CHB][hapmap]
rs17747301	1.00[CHB][hapmap]
rs17832365	1.00[CHB][hapmap]
rs17832371	1.00[AFR][1000 genomes]
rs17832389	1.00[AFR][1000 genomes]
rs2147114	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2274075	1.00[CHB][hapmap]
rs2296181	1.00[CHB][hapmap]
rs28478195	0.81[AMR][1000 genomes]
rs34136598	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34330219	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34446601	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34719936	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35230683	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35294669	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35418987	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35466279	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35536987	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35830444	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736876	1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs3742570	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742571	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45458197	1.00[AFR][1000 genomes]
rs45501402	1.00[AFR][1000 genomes]
rs71412688	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71412689	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71412690	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71413577	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71413578	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7145064	0.80[AMR][1000 genomes]
rs7150841	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs8007065	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs8008528	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs8009239	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs8009608	0.81[AMR][1000 genomes]
rs8019218	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9323289	1.00[CHB][hapmap]
rs9944028	0.81[AMR][1000 genomes]
rs9972177	1.00[CHB][hapmap]
rs9972178	1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs9972180	1.00[CHB][hapmap];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901958	chr14:55822095-56045411	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv901962	chr14:55862956-56101879	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv901963	chr14:55871452-56085130	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv901964	chr14:55871452-56101879	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
7	nsv564874	chr14:55879685-56027815	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1051564	chr14:55895610-56130788	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv542103	chr14:55895610-56130788	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv1047054	chr14:55922287-56035579	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1037161	chr14:55928030-56039353	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv901965	chr14:55976428-56101879	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17745274	KTN1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs17745274	KTN1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55986600-56000600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr14:55996400-55998600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr14:55997600-56000600	Weak transcription	NHEK	skin
4	chr14:55997600-56002400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr14:55997800-55999400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr14:55997800-55999400	Weak transcription	Esophagus	oesophagus
7	chr14:55997800-55999600	Weak transcription	Fetal Heart	heart
8	chr14:55997800-56000600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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