Variant report

Variant	rs229603
Chromosome Location	chr14:65165090-65165091
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	chr14:65163822..65165712-chr14:65213676..65215408,2	MCF-7	breast:
2	chr14:65163365..65166214-chr14:65168108..65170006,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs17179984	1.00[JPT][hapmap]
rs17180090	1.00[JPT][hapmap]
rs17767188	1.00[JPT][hapmap]
rs17767206	1.00[JPT][hapmap]
rs1985465	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1998120	0.89[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs229620	0.88[ASN][1000 genomes]
rs229624	1.00[JPT][hapmap]
rs229625	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs229626	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs229644	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs229646	1.00[JPT][hapmap]
rs229650	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs229651	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs229655	0.88[ASN][1000 genomes]
rs229659	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs229660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs229662	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs229663	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs229664	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs229665	0.88[EUR][1000 genomes]
rs41301473	0.83[ASN][1000 genomes]
rs58789159	0.83[ASN][1000 genomes]
rs73273524	0.83[ASN][1000 genomes]
rs73273534	0.83[ASN][1000 genomes]
rs73273536	0.83[ASN][1000 genomes]
rs73273546	0.92[ASN][1000 genomes]
rs73273549	0.83[ASN][1000 genomes]
rs754435	0.83[ASN][1000 genomes]
rs872296	1.00[JPT][hapmap];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049097	chr14:65027753-65202018	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs229603	PLEKHG3	cis	Whole Blood	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65149400-65169400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr14:65155600-65165200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr14:65156000-65165200	Weak transcription	Fetal Thymus	thymus
4	chr14:65159000-65166000	Enhancers	Brain Hippocampus Middle	brain
5	chr14:65160000-65165600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr14:65160000-65165800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr14:65160000-65168400	Weak transcription	HMEC	breast
8	chr14:65160000-65168600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr14:65160200-65165400	Weak transcription	NHEK	skin
10	chr14:65160800-65166600	Enhancers	Fetal Intestine Small	intestine
11	chr14:65161200-65169200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr14:65161400-65168200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr14:65161600-65165800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr14:65161800-65168400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr14:65162000-65165200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr14:65162000-65167600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr14:65162200-65165200	Weak transcription	Fetal Lung	lung
18	chr14:65162200-65165600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr14:65162200-65169800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr14:65162800-65165600	Enhancers	Brain Substantia Nigra	brain
21	chr14:65162800-65166400	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr14:65162800-65166400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr14:65162800-65166600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr14:65163000-65165800	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr14:65163000-65166400	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr14:65163200-65165800	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr14:65163200-65170600	Weak transcription	Right Ventricle	heart
28	chr14:65163400-65165200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr14:65163400-65165400	Weak transcription	Fetal Kidney	kidney
30	chr14:65163400-65165600	Weak transcription	Colon Smooth Muscle	Colon
31	chr14:65163400-65165800	Weak transcription	Pancreas	Pancrea
32	chr14:65163400-65166200	Enhancers	Primary T cells from cord blood	blood
33	chr14:65163400-65166600	Enhancers	Primary T cells fromperipheralblood	blood
34	chr14:65163400-65167400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr14:65163400-65170400	Weak transcription	Left Ventricle	heart
36	chr14:65163400-65170600	Weak transcription	Right Atrium	heart
37	chr14:65163600-65165400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr14:65163600-65165400	Weak transcription	Brain Angular Gyrus	brain
39	chr14:65163600-65166000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr14:65163600-65168200	Weak transcription	Brain Anterior Caudate	brain
41	chr14:65163600-65170000	Weak transcription	Fetal Heart	heart
42	chr14:65163800-65169600	Weak transcription	Colonic Mucosa	Colon
43	chr14:65164000-65165400	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr14:65164000-65165800	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr14:65164000-65166600	Enhancers	Placenta	Placenta
46	chr14:65164200-65168400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr14:65164400-65165200	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr14:65164400-65166200	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr14:65164400-65166600	Enhancers	Fetal Intestine Large	intestine
50	chr14:65164400-65167200	Enhancers	Primary monocytes fromperipheralblood	blood

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