Variant report

Variant	rs17109189
Chromosome Location	chr14:71709355-71709356
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71708680..71711261-chr14:71786150..71788899,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197555	Chromatin interaction
ENSG00000259146	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1000448	0.99[ASN][1000 genomes]
rs1000449	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158903	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11622499	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11623541	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11623545	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap]
rs11627275	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190863	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4899392	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902924	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs56398258	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7149082	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1044090	chr14:71496198-71780026	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv832827	chr14:71676178-71833519	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17109189	PLEKHH1	cis	cerebellum	SCAN
rs17109189	ACOT1	cis	cerebellum	SCAN
rs17109189	PCNX	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71695800-71709400	Weak transcription	Pancreas	Pancrea
2	chr14:71704600-71713200	Weak transcription	Thymus	Thymus
3	chr14:71706800-71709600	Enhancers	Fetal Lung	lung
4	chr14:71706800-71711800	Enhancers	Fetal Heart	heart
5	chr14:71706800-71713000	Enhancers	Fetal Muscle Leg	muscle
6	chr14:71707200-71712000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr14:71707200-71712000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr14:71707400-71712000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr14:71707600-71712000	Weak transcription	Primary T cells from cord blood	blood
10	chr14:71707600-71712200	Weak transcription	Fetal Thymus	thymus
11	chr14:71707600-71713000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr14:71707800-71712200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr14:71708000-71710000	Enhancers	Colon Smooth Muscle	Colon
14	chr14:71708000-71712400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr14:71708200-71709800	Enhancers	Lung	lung
16	chr14:71708200-71710400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr14:71708200-71712200	Enhancers	NHDF-Ad	bronchial
18	chr14:71708200-71713400	Weak transcription	NHEK	skin
19	chr14:71708400-71709400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr14:71708400-71709600	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr14:71708400-71709800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr14:71708400-71709800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr14:71708400-71711600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr14:71708400-71711600	Enhancers	HSMM	muscle
25	chr14:71708600-71709600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr14:71708600-71709600	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr14:71708600-71709800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr14:71708600-71709800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr14:71708600-71709800	Enhancers	Fetal Stomach	stomach
30	chr14:71708600-71711400	Enhancers	Aorta	Aorta
31	chr14:71708600-71712200	Weak transcription	Spleen	Spleen
32	chr14:71708800-71709400	Enhancers	HUVEC	blood vessel
33	chr14:71708800-71709800	Enhancers	Stomach Smooth Muscle	stomach
34	chr14:71708800-71711600	Enhancers	Muscle Satellite Cultured Cells	--
35	chr14:71709000-71709400	Enhancers	Brain Anterior Caudate	brain
36	chr14:71709000-71709400	Enhancers	Placenta	Placenta
37	chr14:71709000-71709400	Enhancers	Right Atrium	heart
38	chr14:71709000-71709600	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr14:71709000-71709600	Enhancers	Rectal Smooth Muscle	rectum
40	chr14:71709000-71709600	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr14:71709000-71709800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr14:71709000-71709800	Flanking Active TSS	HSMMtube	muscle
43	chr14:71709000-71711200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr14:71709000-71711200	Enhancers	NH-A	brain
45	chr14:71709000-71715200	Weak transcription	Fetal Brain Male	brain
46	chr14:71709200-71711000	Weak transcription	Left Ventricle	heart
47	chr14:71709200-71712200	Enhancers	Osteobl	bone

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