Variant report

Variant	rs13379340
Chromosome Location	chr14:56050346-56050347
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr14:56050275-56050529	GM12878	blood:	n/a	n/a
2	KAP1	chr14:56050300-56051476	HEK293	kidney:	n/a	n/a
3	POLR2A	chr14:56050308-56051496	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:56045115..56047584-chr14:56049131..56050750,2	K562	blood:
2	chr14:56047768..56050679-chr14:56060569..56062105,2	K562	blood:
3	chr14:56050224..56053643-chr14:56057156..56060698,4	MCF-7	breast:
4	chr14:56047540..56051954-chr14:56053859..56059782,6	K562	blood:
5	chr14:56048425..56050750-chr14:56067419..56069440,2	MCF-7	breast:

No data

Variant related genes	Relation type
KTN1-AS1	TF binding region
ENSG00000186615	Chromatin interaction
ENSG00000126777	Chromatin interaction

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

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

rs_ID	r²[population]
rs10083303	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083353	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083431	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083493	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10083499	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10129890	0.89[AMR][1000 genomes]
rs10133729	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10133962	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10135426	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10135600	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10136155	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137364	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137885	0.81[EUR][1000 genomes]
rs10139905	0.81[EUR][1000 genomes]
rs10142497	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10142757	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10143002	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10145687	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10146604	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10147380	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10147431	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10148122	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10148188	0.86[AFR][1000 genomes]
rs10148983	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10149408	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10150498	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10151664	0.85[AMR][1000 genomes]
rs10483643	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483645	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483646	0.84[EUR][1000 genomes]
rs10483648	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483650	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11546	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12100753	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12100949	0.85[AMR][1000 genomes]
rs12323476	0.81[EUR][1000 genomes]
rs12879564	0.84[AMR][1000 genomes]
rs12880362	0.84[AMR][1000 genomes]
rs12883972	0.81[AMR][1000 genomes]
rs12886406	0.84[AMR][1000 genomes]
rs12893061	0.84[AMR][1000 genomes]
rs12893610	0.84[AMR][1000 genomes]
rs12893676	0.84[AMR][1000 genomes]
rs12894368	0.84[AMR][1000 genomes]
rs12894613	0.84[AMR][1000 genomes]
rs13379151	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379264	0.86[AFR][1000 genomes]
rs13379342	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379343	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17253716	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17253723	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17253730	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17253744	0.84[EUR][1000 genomes]
rs17683614	0.88[AMR][1000 genomes]
rs17683626	0.88[AMR][1000 genomes]
rs17683656	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17683728	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17685078	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17685102	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17745459	0.84[AMR][1000 genomes]
rs17746033	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17746106	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17747083	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17747301	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17832365	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17832371	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2147114	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274075	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296181	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28366673	0.86[AFR][1000 genomes]
rs28373835	0.86[AFR][1000 genomes]
rs28375514	0.84[EUR][1000 genomes]
rs28380739	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28392709	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28409547	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28478195	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28513551	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28537145	0.82[EUR][1000 genomes]
rs28539882	0.81[EUR][1000 genomes]
rs28549152	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28581185	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28587929	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28616134	0.84[EUR][1000 genomes]
rs28661008	0.88[EUR][1000 genomes]
rs28663681	0.80[EUR][1000 genomes]
rs28681420	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28754619	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28831725	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34136598	0.84[AMR][1000 genomes]
rs34330219	0.84[AMR][1000 genomes]
rs34446601	0.84[AMR][1000 genomes]
rs34719936	0.84[AMR][1000 genomes]
rs35230683	0.84[AMR][1000 genomes]
rs35294669	0.84[AMR][1000 genomes]
rs35418987	0.84[AMR][1000 genomes]
rs35466279	0.84[AMR][1000 genomes]
rs35536987	0.84[AMR][1000 genomes]
rs35830444	0.84[AMR][1000 genomes]
rs3736876	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742570	0.84[AMR][1000 genomes]
rs3742571	0.81[AMR][1000 genomes]
rs45458197	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45501402	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58569951	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58589065	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71412688	0.84[AMR][1000 genomes]
rs71412689	0.84[AMR][1000 genomes]
rs71412690	0.84[AMR][1000 genomes]
rs71413577	0.84[AMR][1000 genomes]
rs71413578	0.84[AMR][1000 genomes]
rs7145064	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7150841	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74051609	0.83[EUR][1000 genomes]
rs74053651	0.83[EUR][1000 genomes]
rs8006705	0.83[EUR][1000 genomes]
rs8007065	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8008528	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8009239	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8009608	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8013714	0.83[EUR][1000 genomes]
rs8013831	0.83[EUR][1000 genomes]
rs8017891	0.83[EUR][1000 genomes]
rs8018142	0.83[EUR][1000 genomes]
rs8019218	0.80[AMR][1000 genomes]
rs9323289	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944028	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972178	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972180	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[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
rs13379340	KTN1	cis	multi-tissue	Pritchard

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56045600-56051000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr14:56048200-56050600	Weak transcription	Aorta	Aorta
3	chr14:56048200-56054200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr14:56048200-56068400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr14:56048400-56050400	Weak transcription	Placenta	Placenta
6	chr14:56048400-56050600	Weak transcription	Pancreas	Pancrea
7	chr14:56048400-56050800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr14:56048400-56052000	Enhancers	Primary B cells from peripheral blood	blood
9	chr14:56048400-56052800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr14:56048400-56055200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr14:56048400-56056000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr14:56048400-56068400	Weak transcription	Esophagus	oesophagus
13	chr14:56048400-56086000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr14:56048600-56050400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr14:56048600-56050400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr14:56048600-56050400	Weak transcription	Brain Angular Gyrus	brain
17	chr14:56048600-56050400	Weak transcription	Fetal Muscle Leg	muscle
18	chr14:56048600-56050400	Weak transcription	Ovary	ovary
19	chr14:56048600-56050400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr14:56048600-56050400	Weak transcription	Small Intestine	intestine
21	chr14:56048600-56050600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr14:56048600-56050600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr14:56048600-56050600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr14:56048600-56050600	Enhancers	Duodenum Mucosa	Duodenum
25	chr14:56048600-56050600	Weak transcription	Gastric	stomach
26	chr14:56048600-56050600	Weak transcription	Psoas Muscle	Psoas
27	chr14:56048600-56050600	Weak transcription	Spleen	Spleen
28	chr14:56048600-56050800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr14:56048600-56050800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr14:56048600-56050800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr14:56048600-56050800	Weak transcription	Colonic Mucosa	Colon
32	chr14:56048600-56050800	Weak transcription	Fetal Intestine Large	intestine
33	chr14:56048600-56050800	Weak transcription	Left Ventricle	heart
34	chr14:56048600-56051200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr14:56048600-56051200	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr14:56048600-56051400	Enhancers	Primary hematopoietic stem cells	blood
37	chr14:56048600-56051400	Enhancers	Rectal Smooth Muscle	rectum
38	chr14:56048600-56051600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr14:56048600-56051600	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr14:56048600-56052400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr14:56048600-56052400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr14:56048600-56052800	Weak transcription	Thymus	Thymus
43	chr14:56048600-56053000	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr14:56048600-56053600	Enhancers	Osteobl	bone
45	chr14:56048600-56054000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr14:56048600-56055400	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr14:56048600-56055400	Enhancers	Liver	Liver
48	chr14:56048600-56058400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr14:56048600-56060400	Weak transcription	Brain Substantia Nigra	brain
50	chr14:56048600-56070800	Weak transcription	H9 Cell Line	embryonic stem cell

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