Variant report

Variant	rs28380739
Chromosome Location	chr14:56088402-56088403
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:56087704..56089549-chr14:56953257..56955747,2	K562	blood:

Variant related genes	Relation type
ENSG00000070269	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10083303	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083353	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083431	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083493	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10083499	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10129537	0.87[AFR][1000 genomes]
rs10133729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10133962	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10135426	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10135600	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10136155	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137340	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137364	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137885	0.85[EUR][1000 genomes]
rs10139905	0.85[EUR][1000 genomes]
rs10142497	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10142757	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10142869	0.83[AFR][1000 genomes]
rs10143002	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10145687	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10146604	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10147380	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10147431	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10148122	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10148983	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10149408	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10150498	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483645	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483646	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10483648	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483650	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11546	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12100753	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12323476	0.85[EUR][1000 genomes]
rs12879564	0.80[AMR][1000 genomes]
rs12880362	0.80[AMR][1000 genomes]
rs12886406	0.80[AMR][1000 genomes]
rs12893061	0.80[AMR][1000 genomes]
rs12893610	0.80[AMR][1000 genomes]
rs12893676	0.80[AMR][1000 genomes]
rs12894368	0.80[AMR][1000 genomes]
rs12894613	0.80[AMR][1000 genomes]
rs13379151	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379340	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379342	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379343	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379353	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17253716	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17253723	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17253730	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17253744	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17683614	0.84[AMR][1000 genomes]
rs17683626	0.84[AMR][1000 genomes]
rs17683656	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17683728	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17685078	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17685102	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17745459	0.80[AMR][1000 genomes]
rs17746033	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17746106	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17747083	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17747301	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17832365	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17832371	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2147114	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296181	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28375514	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28392709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28409547	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28478195	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28513551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28537145	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28539882	0.85[EUR][1000 genomes]
rs28549152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28581185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28587929	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28616134	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28661008	0.85[EUR][1000 genomes]
rs28663681	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28681420	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28754619	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28831725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34136598	0.80[AMR][1000 genomes]
rs34330219	0.80[AMR][1000 genomes]
rs34446601	0.80[AMR][1000 genomes]
rs34719936	0.80[AMR][1000 genomes]
rs35230683	0.80[AMR][1000 genomes]
rs35294669	0.80[AMR][1000 genomes]
rs35418987	0.80[AMR][1000 genomes]
rs35466279	0.80[AMR][1000 genomes]
rs35536987	0.80[AMR][1000 genomes]
rs35830444	0.80[AMR][1000 genomes]
rs3736876	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742570	0.80[AMR][1000 genomes]
rs45458197	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45501402	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58569951	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58589065	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71412688	0.80[AMR][1000 genomes]
rs71412689	0.80[AMR][1000 genomes]
rs71412690	0.80[AMR][1000 genomes]
rs71413577	0.80[AMR][1000 genomes]
rs71413578	0.80[AMR][1000 genomes]
rs7145064	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7150841	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74051609	0.86[EUR][1000 genomes]
rs74053651	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8006705	0.86[EUR][1000 genomes]
rs8007065	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8008528	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8009239	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8009608	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8013714	0.86[EUR][1000 genomes]
rs8013831	0.86[EUR][1000 genomes]
rs8017891	0.86[EUR][1000 genomes]
rs8018142	0.86[EUR][1000 genomes]
rs9323289	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944028	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972177	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972178	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972180	0.92[AMR][1000 genomes];0.96[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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	esv3338673	chr14:56088012-56088652	Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28380739	KTN1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56077800-56092000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr14:56078600-56148600	Weak transcription	Stomach Mucosa	stomach
3	chr14:56078800-56095400	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr14:56079000-56089000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr14:56079000-56091000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr14:56079200-56095200	Strong transcription	Primary T cells from cord blood	blood
7	chr14:56079800-56111400	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr14:56080200-56097800	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr14:56080600-56091800	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr14:56080800-56110800	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr14:56081200-56090400	Strong transcription	Adipose Nuclei	Adipose
12	chr14:56081600-56090000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr14:56082200-56091000	Strong transcription	Placenta	Placenta
14	chr14:56082400-56090200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr14:56082400-56091800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr14:56082400-56092000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr14:56082600-56089600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr14:56082600-56091800	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr14:56082800-56090000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr14:56082800-56090200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr14:56082800-56090400	Strong transcription	Osteobl	bone
22	chr14:56082800-56090600	Strong transcription	NHEK	skin
23	chr14:56082800-56091800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr14:56083000-56091000	Strong transcription	HUVEC	blood vessel
25	chr14:56083200-56090000	Strong transcription	NH-A	brain
26	chr14:56083800-56089200	Weak transcription	Fetal Heart	heart
27	chr14:56084000-56091800	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr14:56084800-56088600	Strong transcription	Placenta Amnion	Placenta Amnion
29	chr14:56085000-56091000	Strong transcription	Left Ventricle	heart
30	chr14:56085200-56090000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr14:56086000-56093400	Strong transcription	A549	lung
32	chr14:56086600-56092400	Weak transcription	HMEC	breast
33	chr14:56086800-56094400	Weak transcription	NHDF-Ad	bronchial
34	chr14:56087200-56088600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
35	chr14:56087200-56091800	Strong transcription	Brain Angular Gyrus	brain
36	chr14:56087400-56088600	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr14:56087400-56088600	Strong transcription	Brain Anterior Caudate	brain
38	chr14:56087400-56088800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr14:56087400-56089000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr14:56087400-56089000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr14:56087400-56089800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr14:56087400-56091000	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr14:56087400-56091200	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr14:56087400-56091600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr14:56087400-56091800	Strong transcription	Fetal Muscle Trunk	muscle
46	chr14:56087400-56091800	Strong transcription	Fetal Muscle Leg	muscle
47	chr14:56087400-56092000	Strong transcription	Liver	Liver
48	chr14:56087400-56092000	Strong transcription	Fetal Intestine Large	intestine
49	chr14:56087400-56092000	Strong transcription	Fetal Stomach	stomach
50	chr14:56087400-56092800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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