Variant report

Variant	rs28587929
Chromosome Location	chr14:56097492-56097493
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	chr14:56096758..56098924-chr14:56100584..56102581,2	K562	blood:

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10083303	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083353	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083431	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083493	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10083499	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10129890	0.81[AMR][1000 genomes]
rs10133729	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10133962	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10135426	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10135600	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10136155	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137340	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137364	1.00[AFR][1000 genomes];0.92[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	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10142757	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10143002	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10145687	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10146604	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10147380	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10147431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10148122	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10148983	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10149408	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10150498	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483643	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483645	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483646	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10483648	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483650	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11546	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12100753	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12323476	0.85[EUR][1000 genomes]
rs13379151	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379340	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379342	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379343	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379353	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17253716	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17253723	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17253730	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17253744	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17683614	0.80[AMR][1000 genomes]
rs17683626	0.80[AMR][1000 genomes]
rs17683656	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17683728	0.89[AFR][1000 genomes];0.88[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	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17746033	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17746106	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17747083	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17747301	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17832365	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17832371	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2147114	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274075	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296181	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28375514	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28380739	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28392709	0.89[AFR][1000 genomes];0.96[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	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28513551	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28537145	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28539882	0.85[EUR][1000 genomes]
rs28549152	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28581185	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28616134	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28661008	0.85[EUR][1000 genomes]
rs28663681	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28681420	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28754619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28831725	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736876	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45458197	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45501402	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58569951	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58589065	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7145064	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7150841	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74051609	0.86[EUR][1000 genomes]
rs74053651	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8006705	0.86[EUR][1000 genomes]
rs8007065	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8008528	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8009239	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8009608	0.89[AFR][1000 genomes];0.88[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	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944028	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972177	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972178	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972180	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28587929	KTN1	cis	multi-tissue	Pritchard

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	chr14:56079800-56111400	Strong transcription	Rectal Mucosa Donor 29	rectum
3	chr14:56080200-56097800	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr14:56080800-56110800	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr14:56087400-56111800	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr14:56087400-56112200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr14:56087400-56132200	Strong transcription	Dnd41	blood
8	chr14:56087600-56099000	Strong transcription	Primary B cells from peripheral blood	blood
9	chr14:56087600-56099400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr14:56087600-56100400	Weak transcription	Right Ventricle	heart
11	chr14:56087600-56100600	Weak transcription	Fetal Intestine Small	intestine
12	chr14:56087600-56101400	Weak transcription	Pancreas	Pancrea
13	chr14:56087600-56107400	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr14:56087600-56110000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr14:56087600-56145200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr14:56088000-56101200	Weak transcription	Esophagus	oesophagus
17	chr14:56088000-56101600	Weak transcription	Fetal Brain Male	brain
18	chr14:56088000-56103600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr14:56088200-56098600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr14:56088200-56104000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr14:56088200-56108600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr14:56088200-56129400	Weak transcription	Spleen	Spleen
23	chr14:56088200-56132200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr14:56088400-56103600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr14:56088400-56121600	Weak transcription	Aorta	Aorta
26	chr14:56088400-56121800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr14:56088400-56153200	Weak transcription	Gastric	stomach
28	chr14:56088600-56101400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr14:56088600-56103600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr14:56090400-56101400	Weak transcription	Brain Germinal Matrix	brain
31	chr14:56090800-56107000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr14:56091200-56104800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr14:56091600-56100600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr14:56091600-56102000	Weak transcription	Colonic Mucosa	Colon
35	chr14:56091800-56100400	Weak transcription	Lung	lung
36	chr14:56091800-56101400	Weak transcription	Brain Angular Gyrus	brain
37	chr14:56092000-56100600	Weak transcription	Fetal Stomach	stomach
38	chr14:56092000-56101200	Weak transcription	Psoas Muscle	Psoas
39	chr14:56092800-56099200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr14:56092800-56135400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr14:56093200-56110000	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr14:56093400-56098200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr14:56093400-56102600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr14:56093400-56105000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr14:56093400-56107600	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr14:56093600-56097600	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr14:56093600-56099200	Strong transcription	Primary B cells from cord blood	blood
48	chr14:56093800-56098400	Strong transcription	Osteobl	bone
49	chr14:56093800-56098600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr14:56093800-56104400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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