Variant report

Variant	rs8018142
Chromosome Location	chr14:56173288-56173289
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	chr14:56172874..56174577-chr14:56174772..56176710,2	MCF-7	breast:
2	chr14:55890007..55892259-chr14:56172820..56174391,2	K562	blood:

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10083303	0.90[EUR][1000 genomes]
rs10083353	0.88[EUR][1000 genomes]
rs10083431	0.92[EUR][1000 genomes]
rs10083493	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs10083499	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs10133729	0.86[EUR][1000 genomes]
rs10133962	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs10135426	0.83[EUR][1000 genomes]
rs10135600	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10136155	0.83[EUR][1000 genomes]
rs10137340	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs10137364	0.86[EUR][1000 genomes]
rs10137885	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10139905	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10142497	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs10142757	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs10143002	1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs10145687	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10147380	0.83[EUR][1000 genomes]
rs10147431	0.86[EUR][1000 genomes]
rs10148122	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10148983	0.90[EUR][1000 genomes]
rs10150498	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs10483643	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs10483645	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10483646	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10483648	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10483650	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11546	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12100753	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs12100949	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs12323476	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12892022	1.00[CHB][hapmap]
rs12894368	1.00[CHB][hapmap]
rs13379151	0.83[EUR][1000 genomes]
rs13379340	0.83[EUR][1000 genomes]
rs13379342	0.83[EUR][1000 genomes]
rs13379343	0.83[EUR][1000 genomes]
rs13379353	0.86[EUR][1000 genomes]
rs17253716	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17253723	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17253730	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17253744	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17683614	1.00[CHB][hapmap]
rs17683626	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs17683656	0.83[EUR][1000 genomes]
rs17683728	0.90[EUR][1000 genomes]
rs17685078	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs17685102	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17745459	1.00[CHB][hapmap]
rs17746033	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs17746106	0.96[EUR][1000 genomes]
rs17747083	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17747301	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17832365	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17832371	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2147114	0.86[EUR][1000 genomes]
rs2274075	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs2296181	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28375514	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28380739	0.86[EUR][1000 genomes]
rs28392709	0.86[EUR][1000 genomes]
rs28478195	0.81[EUR][1000 genomes]
rs28513551	0.86[EUR][1000 genomes]
rs28537145	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28539882	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28549152	0.86[EUR][1000 genomes]
rs28581185	0.86[EUR][1000 genomes]
rs28587929	0.86[EUR][1000 genomes]
rs28616134	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28661008	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28663681	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28681420	0.86[EUR][1000 genomes]
rs28754619	0.86[EUR][1000 genomes]
rs28831725	0.86[EUR][1000 genomes]
rs3736876	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs45458197	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs45501402	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58569951	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58589065	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7145064	0.86[EUR][1000 genomes]
rs7150841	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs74051609	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74053651	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8006705	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8007065	0.86[EUR][1000 genomes]
rs8008528	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs8009239	0.86[EUR][1000 genomes]
rs8009608	0.83[EUR][1000 genomes]
rs8013714	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8013831	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8017891	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9323289	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9944028	0.90[EUR][1000 genomes]
rs9972177	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs9972178	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs9972180	1.00[CHB][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv901966	chr14:56160904-56436203	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8018142	KTN1	cis	multi-tissue	Pritchard

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56102400-56185400	Weak transcription	Right Ventricle	heart
2	chr14:56148000-56174000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr14:56153400-56174000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr14:56153800-56173800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr14:56153800-56174000	Weak transcription	Brain Anterior Caudate	brain
6	chr14:56154000-56173800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr14:56154000-56177800	Weak transcription	Left Ventricle	heart
8	chr14:56154000-56191000	Weak transcription	Aorta	Aorta
9	chr14:56154400-56177800	Weak transcription	Fetal Muscle Leg	muscle
10	chr14:56154800-56174000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr14:56155600-56173600	Weak transcription	Primary T cells from cord blood	blood
12	chr14:56157600-56178000	Weak transcription	Psoas Muscle	Psoas
13	chr14:56157600-56180000	Weak transcription	Primary B cells from cord blood	blood
14	chr14:56162800-56174000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr14:56164600-56179600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr14:56166200-56173800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr14:56166400-56173600	Weak transcription	NHLF	lung
18	chr14:56168600-56174600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr14:56169000-56177400	Weak transcription	Osteobl	bone
20	chr14:56169600-56173600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr14:56169600-56182400	Weak transcription	GM12878-XiMat	blood
22	chr14:56169800-56174000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr14:56170000-56182400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr14:56170400-56182400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr14:56170800-56177800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr14:56171400-56174000	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr14:56171800-56174000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr14:56171800-56174000	Enhancers	Fetal Intestine Large	intestine
29	chr14:56171800-56174000	Enhancers	Fetal Intestine Small	intestine
30	chr14:56171800-56174000	Enhancers	HMEC	breast
31	chr14:56171800-56175000	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr14:56172000-56174600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr14:56172200-56173400	Enhancers	NHEK	skin
34	chr14:56172200-56174000	Enhancers	Thymus	Thymus
35	chr14:56172200-56174200	Enhancers	Fetal Thymus	thymus
36	chr14:56172200-56174600	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr14:56172200-56182200	Weak transcription	HSMM	muscle
38	chr14:56172600-56182200	Weak transcription	HSMMtube	muscle
39	chr14:56172800-56173400	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr14:56172800-56173400	Enhancers	Stomach Mucosa	stomach
41	chr14:56172800-56174400	Enhancers	A549	lung
42	chr14:56173200-56174000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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