Variant report

Variant	rs45501402
Chromosome Location	chr14:56140115-56140116
allele	C/T
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	E2F4	chr14:56139878-56140199	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:56135952..56138303-chr14:56139128..56140660,2	MCF-7	breast:
2	chr14:56136295..56138118-chr14:56139376..56142156,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FBXO34-2	chr14:56139647-56141022	NONHSAT037020

Variant related genes	Relation type
KTN1	TF binding region
ENSG00000126777	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10083303	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083353	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083431	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083493	0.84[EUR][1000 genomes]
rs10083499	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10133729	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10133962	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10135426	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10135600	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10136155	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137340	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137364	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137885	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10139905	0.88[EUR][1000 genomes]
rs10142497	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10142757	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10143002	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10145687	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10146604	0.84[EUR][1000 genomes]
rs10147380	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10147431	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10148122	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10148983	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10149408	0.84[EUR][1000 genomes]
rs10150498	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483643	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10483648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11546	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12100753	0.83[EUR][1000 genomes]
rs12323476	0.88[EUR][1000 genomes]
rs12886406	1.00[AFR][1000 genomes]
rs12892022	1.00[AFR][1000 genomes]
rs12892413	1.00[AFR][1000 genomes]
rs12893081	1.00[AFR][1000 genomes]
rs12893836	1.00[AFR][1000 genomes]
rs13379151	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379340	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379342	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379343	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379353	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17253716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17253723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17253730	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17253744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17253792	0.87[AMR][1000 genomes]
rs17683614	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17683626	0.83[AMR][1000 genomes]
rs17683656	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17683728	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17685078	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17685102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17744929	1.00[AFR][1000 genomes]
rs17745274	1.00[AFR][1000 genomes]
rs17745459	1.00[AFR][1000 genomes]
rs17746033	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17746106	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17747083	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17747301	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17832365	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17832371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17832389	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2147114	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274075	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296181	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28375514	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28380739	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28392709	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28409547	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28478195	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28513551	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28537145	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28539882	0.88[EUR][1000 genomes]
rs28549152	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28581185	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28587929	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28616134	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28661008	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28663681	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28681420	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28754619	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28831725	0.84[AMR][1000 genomes];0.92[EUR][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[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45458197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58569951	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58589065	0.85[AMR][1000 genomes];0.96[EUR][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]
rs7145064	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7150841	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74051609	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs74053651	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8006705	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8007065	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8008528	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8009239	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8009608	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8010475	0.87[AMR][1000 genomes]
rs8013714	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8013831	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8017891	0.90[EUR][1000 genomes]
rs8018142	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9323289	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944028	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972177	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972178	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972180	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	esv1792376	chr14:56108007-56150151	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1283	chr14:56120059-56164729	Strong transcription Genic enhancers ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs45501402	KTN1	cis	multi-tissue	Pritchard
rs45501402	KTN1-AS1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56078600-56148600	Weak transcription	Stomach Mucosa	stomach
2	chr14:56087600-56145200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr14:56088400-56153200	Weak transcription	Gastric	stomach
4	chr14:56095000-56142200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr14:56097600-56145200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr14:56097600-56155400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr14:56101800-56162800	Weak transcription	Brain Germinal Matrix	brain
8	chr14:56102400-56145200	Weak transcription	Lung	lung
9	chr14:56102400-56185400	Weak transcription	Right Ventricle	heart
10	chr14:56104800-56157400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr14:56106000-56150200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr14:56109200-56141800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr14:56109200-56164000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr14:56109800-56145400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr14:56113800-56155000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr14:56115000-56155000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr14:56122000-56145400	Weak transcription	Pancreas	Pancrea
18	chr14:56122400-56145000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr14:56122400-56145400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr14:56122400-56152600	Weak transcription	Esophagus	oesophagus
21	chr14:56122400-56164800	Weak transcription	Small Intestine	intestine
22	chr14:56124000-56142200	Weak transcription	Fetal Kidney	kidney
23	chr14:56125000-56144600	Weak transcription	Fetal Muscle Leg	muscle
24	chr14:56128200-56145200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr14:56128200-56149800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr14:56129200-56143800	Weak transcription	Fetal Intestine Small	intestine
27	chr14:56129200-56144600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr14:56129200-56145200	Weak transcription	Fetal Stomach	stomach
29	chr14:56129800-56145000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr14:56129800-56145200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr14:56129800-56145200	Weak transcription	Spleen	Spleen
32	chr14:56129800-56152000	Weak transcription	Aorta	Aorta
33	chr14:56130400-56145200	Weak transcription	Ovary	ovary
34	chr14:56131400-56145200	Weak transcription	Fetal Brain Male	brain
35	chr14:56131400-56145200	Weak transcription	Thymus	Thymus
36	chr14:56133000-56145200	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr14:56133400-56144000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr14:56133400-56145200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr14:56133400-56153400	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr14:56134000-56143600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr14:56134000-56155000	Strong transcription	HSMM	muscle
42	chr14:56134200-56153600	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr14:56134600-56154200	Strong transcription	Liver	Liver
44	chr14:56134800-56145000	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr14:56134800-56148200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr14:56135000-56153400	Strong transcription	Placenta	Placenta
47	chr14:56135200-56152800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr14:56135200-56153600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr14:56135600-56141000	Weak transcription	Left Ventricle	heart
50	chr14:56135600-56145400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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