Variant report

Variant	rs17683728
Chromosome Location	chr14:56060389-56060390
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:56056459..56058091-chr14:56059741..56061406,2	MCF-7	breast:
2	chr14:56052261..56055376-chr14:56058166..56061190,4	K562	blood:
3	chr14:56057726..56060571-chr14:56061645..56063881,2	K562	blood:
4	chr14:55847857..55850141-chr14:56058173..56060941,2	MCF-7	breast:
5	chr14:56050224..56053643-chr14:56057156..56060698,4	MCF-7	breast:

Extended variants
information (count: 139 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10083303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083431	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083493	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10083499	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10129537	0.87[AFR][1000 genomes]
rs10129890	0.85[AMR][1000 genomes]
rs10133729	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10133962	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10135426	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10135600	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10136155	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137340	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137364	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137885	0.88[EUR][1000 genomes]
rs10139905	0.88[EUR][1000 genomes]
rs10142497	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10142757	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10142869	0.83[AFR][1000 genomes]
rs10143002	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10145687	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10146604	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10147380	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10147431	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10148122	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10148983	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10149408	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10150498	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10151664	0.82[AMR][1000 genomes]
rs10483643	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483645	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483646	0.92[EUR][1000 genomes]
rs10483648	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483650	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11546	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12100753	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12100949	0.82[AMR][1000 genomes]
rs12323476	0.88[EUR][1000 genomes]
rs12879564	0.88[AMR][1000 genomes]
rs12879705	0.81[AMR][1000 genomes]
rs12880362	0.88[AMR][1000 genomes]
rs12883972	0.84[AMR][1000 genomes]
rs12886406	0.88[AMR][1000 genomes]
rs12893061	0.88[AMR][1000 genomes]
rs12893610	0.88[AMR][1000 genomes]
rs12893676	0.88[AMR][1000 genomes]
rs12894368	0.88[AMR][1000 genomes]
rs12894613	0.88[AMR][1000 genomes]
rs13379151	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379340	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379342	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379343	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379353	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17253716	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17253723	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17253730	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17253744	0.92[EUR][1000 genomes]
rs17683614	0.92[AMR][1000 genomes]
rs17683626	0.92[AMR][1000 genomes]
rs17683656	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17685078	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17685102	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17745274	0.81[AMR][1000 genomes]
rs17745459	0.88[AMR][1000 genomes]
rs17746033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17746106	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17747083	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17747301	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17832365	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17832371	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2147114	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274075	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296181	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28375514	0.92[EUR][1000 genomes]
rs28380739	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28392709	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28409547	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28478195	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28513551	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28537145	0.90[EUR][1000 genomes]
rs28539882	0.88[EUR][1000 genomes]
rs28549152	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28581185	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28587929	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28616134	0.92[EUR][1000 genomes]
rs28661008	0.88[EUR][1000 genomes]
rs28663681	0.88[EUR][1000 genomes]
rs28681420	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28754619	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28831725	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34136598	0.88[AMR][1000 genomes]
rs34330219	0.88[AMR][1000 genomes]
rs34446601	0.88[AMR][1000 genomes]
rs34719936	0.88[AMR][1000 genomes]
rs35230683	0.88[AMR][1000 genomes]
rs35294669	0.88[AMR][1000 genomes]
rs35418987	0.88[AMR][1000 genomes]
rs35466279	0.88[AMR][1000 genomes]
rs35536987	0.88[AMR][1000 genomes]
rs35830444	0.88[AMR][1000 genomes]
rs3736876	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742570	0.88[AMR][1000 genomes]
rs3742571	0.84[AMR][1000 genomes]
rs45458197	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45501402	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58569951	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58589065	0.96[EUR][1000 genomes]
rs71412688	0.88[AMR][1000 genomes]
rs71412689	0.88[AMR][1000 genomes]
rs71412690	0.88[AMR][1000 genomes]
rs71413577	0.88[AMR][1000 genomes]
rs71413578	0.88[AMR][1000 genomes]
rs7145064	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7150841	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74051609	0.90[EUR][1000 genomes]
rs74053651	0.90[EUR][1000 genomes]
rs8006705	0.90[EUR][1000 genomes]
rs8007065	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8008528	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8009239	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8009608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8013714	0.90[EUR][1000 genomes]
rs8013831	0.90[EUR][1000 genomes]
rs8017891	0.90[EUR][1000 genomes]
rs8018142	0.90[EUR][1000 genomes]
rs8019218	0.84[AMR][1000 genomes]
rs9323289	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944028	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972177	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972178	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972180	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17683728	KTN1	cis	multi-tissue	Pritchard

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56048200-56068400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr14:56048400-56068400	Weak transcription	Esophagus	oesophagus
3	chr14:56048400-56086000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr14:56048600-56060400	Weak transcription	Brain Substantia Nigra	brain
5	chr14:56048600-56070800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr14:56051200-56066200	Weak transcription	Colonic Mucosa	Colon
7	chr14:56051200-56069000	Weak transcription	Primary B cells from cord blood	blood
8	chr14:56051600-56061600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr14:56052000-56066200	Weak transcription	Pancreas	Pancrea
10	chr14:56052000-56068400	Weak transcription	Left Ventricle	heart
11	chr14:56052000-56080200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr14:56053200-56069400	Weak transcription	Aorta	Aorta
13	chr14:56054000-56060400	Weak transcription	Ovary	ovary
14	chr14:56055200-56066400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr14:56055200-56069200	Weak transcription	Primary T cells from cord blood	blood
16	chr14:56055400-56061600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr14:56055400-56061600	Weak transcription	Fetal Intestine Small	intestine
18	chr14:56055400-56065800	Weak transcription	Fetal Lung	lung
19	chr14:56055800-56060600	Weak transcription	NH-A	brain
20	chr14:56055800-56067200	Weak transcription	HSMMtube	muscle
21	chr14:56056000-56060400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr14:56056000-56060800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr14:56056000-56067000	Weak transcription	NHDF-Ad	bronchial
24	chr14:56056200-56060400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr14:56056200-56060400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr14:56056200-56060600	Weak transcription	NHEK	skin
27	chr14:56056200-56067200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr14:56056200-56067200	Weak transcription	Adipose Nuclei	Adipose
29	chr14:56056200-56067200	Weak transcription	HMEC	breast
30	chr14:56056200-56068400	Weak transcription	Right Ventricle	heart
31	chr14:56056200-56076000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr14:56056400-56060400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr14:56056400-56060600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr14:56056400-56066000	Weak transcription	Psoas Muscle	Psoas
35	chr14:56056400-56067000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr14:56056400-56067000	Weak transcription	HSMM	muscle
37	chr14:56056400-56067200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr14:56056400-56067200	Weak transcription	NHLF	lung
39	chr14:56057200-56061200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr14:56057200-56065400	Enhancers	HepG2	liver
41	chr14:56057800-56060600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr14:56057800-56061000	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr14:56057800-56061000	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr14:56057800-56061000	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr14:56057800-56061200	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr14:56058000-56060800	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr14:56058400-56062000	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr14:56058600-56060400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr14:56058600-56060600	Enhancers	Hela-S3	cervix
50	chr14:56058600-56064200	Enhancers	Liver	Liver

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