Variant report

Variant	rs229660
Chromosome Location	chr14:65174586-65174587
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:65174479..65176413-chr14:65184169..65186446,2	K562	blood:
2	chr14:65168373..65176902-chr14:65220182..65231670,21	MCF-7	breast:
3	chr14:65168529..65178400-chr14:65179583..65195815,52	MCF-7	breast:
4	chr14:65170433..65175465-chr14:65207632..65214317,8	MCF-7	breast:
5	chr14:65168335..65178043-chr14:65220677..65234710,31	MCF-7	breast:
6	chr14:65173952..65176818-chr14:65213044..65215895,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070182	Chromatin interaction
ENSG00000126822	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs17179984	1.00[JPT][hapmap]
rs17180090	1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs17767188	1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs17767206	0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs1985465	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1985466	0.88[ASN][1000 genomes]
rs1998120	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs229603	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs229624	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs229625	1.00[JPT][hapmap]
rs229626	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs229644	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs229646	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs229650	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs229651	1.00[JPT][hapmap]
rs229659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229662	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs229663	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs229664	1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs229665	0.86[EUR][1000 genomes]
rs41301473	0.83[ASN][1000 genomes]
rs58789159	0.83[ASN][1000 genomes]
rs73273513	0.88[ASN][1000 genomes]
rs73273517	0.92[ASN][1000 genomes]
rs73273524	0.83[ASN][1000 genomes]
rs73273534	0.83[ASN][1000 genomes]
rs73273536	0.83[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:2 , 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
2	esv1818582	chr14:65172898-65256685	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs229660	PLEKHG3	cis	multi-tissue	Pritchard
rs229660	PLEKHG3	cis	Whole Blood	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65170000-65176600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr14:65171800-65177200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr14:65172200-65174600	Flanking Active TSS	HepG2	liver
4	chr14:65172400-65174800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr14:65172400-65174800	Weak transcription	Lung	lung
6	chr14:65172400-65175200	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr14:65172400-65176800	Enhancers	Small Intestine	intestine
8	chr14:65172600-65174800	Weak transcription	HUVEC	blood vessel
9	chr14:65172600-65175000	Enhancers	NHLF	lung
10	chr14:65172600-65175200	Flanking Active TSS	Brain Hippocampus Middle	brain
11	chr14:65172800-65174600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr14:65172800-65174600	Enhancers	Right Ventricle	heart
13	chr14:65172800-65174800	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr14:65172800-65175000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr14:65172800-65175000	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr14:65172800-65175200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr14:65172800-65175200	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr14:65172800-65175600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr14:65172800-65176400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr14:65172800-65176400	Enhancers	Stomach Mucosa	stomach
21	chr14:65172800-65178000	Enhancers	Fetal Heart	heart
22	chr14:65173000-65175000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr14:65173000-65175200	Enhancers	Primary hematopoietic stem cells	blood
24	chr14:65173000-65175200	Enhancers	Placenta	Placenta
25	chr14:65173000-65176400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr14:65173000-65177000	Enhancers	Pancreas	Pancrea
27	chr14:65173000-65177000	Enhancers	Right Atrium	heart
28	chr14:65173000-65177600	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr14:65173200-65174600	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr14:65173200-65174600	Enhancers	NH-A	brain
31	chr14:65173200-65175000	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr14:65173200-65175600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr14:65173200-65175800	Enhancers	Brain Germinal Matrix	brain
34	chr14:65173200-65176400	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr14:65173200-65177000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr14:65173200-65178000	Enhancers	Spleen	Spleen
37	chr14:65173400-65174600	Enhancers	Aorta	Aorta
38	chr14:65173400-65174800	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr14:65173400-65175000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr14:65173400-65175000	Flanking Active TSS	NHEK	skin
41	chr14:65173400-65175600	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr14:65173400-65178000	Enhancers	Adipose Nuclei	Adipose
43	chr14:65173600-65174600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr14:65173600-65174600	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr14:65173600-65174800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr14:65173600-65174800	Enhancers	Primary B cells from cord blood	blood
47	chr14:65173600-65175000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr14:65173600-65175000	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr14:65173600-65175200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr14:65173600-65175200	Enhancers	Rectal Mucosa Donor 31	rectum

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