Variant report

Variant	rs28616134
Chromosome Location	chr14:56178802-56178803
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	chr14:55737454..55740283-chr14:56178729..56181502,2	MCF-7	breast:
2	chr14:56178438..56180249-chr14:56182200..56183742,2	K562	blood:

Variant related genes	Relation type
ENSG00000178974	Chromatin interaction
ENSG00000258413	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10083303	0.92[EUR][1000 genomes]
rs10083353	0.90[EUR][1000 genomes]
rs10083431	0.90[EUR][1000 genomes]
rs10083499	0.92[EUR][1000 genomes]
rs10133729	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10133962	0.92[EUR][1000 genomes]
rs10135426	0.84[EUR][1000 genomes]
rs10135600	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10136155	0.84[EUR][1000 genomes]
rs10137340	0.84[EUR][1000 genomes]
rs10137364	0.88[EUR][1000 genomes]
rs10137885	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10139905	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10142497	0.82[EUR][1000 genomes]
rs10142757	0.84[EUR][1000 genomes]
rs10143002	0.84[EUR][1000 genomes]
rs10145687	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10147380	0.84[EUR][1000 genomes]
rs10147431	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10148122	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10148983	0.84[EUR][1000 genomes]
rs10150498	0.92[EUR][1000 genomes]
rs10483643	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10483645	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10483646	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10483648	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10483650	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11546	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12323476	0.88[EUR][1000 genomes]
rs13379151	0.84[EUR][1000 genomes]
rs13379340	0.84[EUR][1000 genomes]
rs13379342	0.84[EUR][1000 genomes]
rs13379343	0.84[EUR][1000 genomes]
rs13379353	0.84[EUR][1000 genomes]
rs17253716	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17253723	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17253730	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17253744	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17253792	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17683614	0.83[AMR][1000 genomes]
rs17683626	0.83[AMR][1000 genomes]
rs17683656	0.84[EUR][1000 genomes]
rs17683728	0.92[EUR][1000 genomes]
rs17685078	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17685102	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17746033	0.92[EUR][1000 genomes]
rs17746106	0.86[EUR][1000 genomes]
rs17747083	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17747301	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17832365	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17832371	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17832389	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2147114	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2274075	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2296181	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28375514	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28380739	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28392709	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28409547	0.80[EUR][1000 genomes]
rs28478195	0.82[EUR][1000 genomes]
rs28513551	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28537145	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28539882	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28549152	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28581185	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28587929	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28661008	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28663681	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28681420	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28754619	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28831725	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3736876	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs45458197	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs45501402	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58569951	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58589065	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7145064	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7150841	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs74051609	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs74053651	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8006705	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8007065	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8008528	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8009239	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8009608	0.85[EUR][1000 genomes]
rs8010475	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8013714	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8013831	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][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];0.88[EUR][1000 genomes]
rs9944028	0.84[EUR][1000 genomes]
rs9972177	0.84[EUR][1000 genomes]
rs9972178	0.84[EUR][1000 genomes]
rs9972180	0.84[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
rs28616134	KTN1	cis	multi-tissue	Pritchard

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56102400-56185400	Weak transcription	Right Ventricle	heart
2	chr14:56154000-56191000	Weak transcription	Aorta	Aorta
3	chr14:56157600-56180000	Weak transcription	Primary B cells from cord blood	blood
4	chr14:56164600-56179600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr14:56169600-56182400	Weak transcription	GM12878-XiMat	blood
6	chr14:56170000-56182400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr14:56170400-56182400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr14:56172200-56182200	Weak transcription	HSMM	muscle
9	chr14:56172600-56182200	Weak transcription	HSMMtube	muscle
10	chr14:56174200-56182400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr14:56174600-56179000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr14:56174600-56179200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr14:56174600-56179200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr14:56174600-56179600	Weak transcription	Brain Anterior Caudate	brain
15	chr14:56174600-56182400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr14:56174800-56179200	Weak transcription	Brain Substantia Nigra	brain
17	chr14:56175600-56179000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr14:56178000-56180000	Enhancers	Psoas Muscle	Psoas
19	chr14:56178000-56182400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr14:56178000-56182400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr14:56178200-56179400	Weak transcription	Fetal Stomach	stomach
22	chr14:56178200-56183400	Weak transcription	Left Ventricle	heart
23	chr14:56178400-56181200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr14:56178400-56182400	Weak transcription	NHLF	lung
25	chr14:56178600-56180600	Enhancers	Placenta	Placenta

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