Variant report

Variant	rs8017407
Chromosome Location	chr14:65037526-65037527
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:65035525..65037855-chr14:65039910..65042725,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10138919	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1040612	1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10431708	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10498515	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10873175	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11158546	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1256146	0.88[CEU][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs1256150	0.84[EUR][1000 genomes]
rs12589307	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12589322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12894050	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12894807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1453005	0.83[EUR][1000 genomes]
rs1901737	0.81[EUR][1000 genomes]
rs2038270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2123461	0.92[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2218994	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs34616731	0.81[EUR][1000 genomes]
rs4902288	0.85[EUR][1000 genomes]
rs4902295	1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4902296	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4902297	1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4902298	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4902299	0.82[CHB][hapmap]
rs7141346	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7148289	1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7149152	0.88[CEU][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7156953	0.87[CEU][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7159809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs761547	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8003734	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8007313	0.90[CHB][hapmap]
rs8016170	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8016361	0.88[CEU][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8018169	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8022447	0.88[CEU][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs926802	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9671381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs971736	0.82[CHB][hapmap]

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
rs8017407	PLEKHG3	cis	multi-tissue	Pritchard

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65021600-65047600	Weak transcription	Pancreas	Pancrea
2	chr14:65028200-65039400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr14:65029400-65039400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr14:65030600-65039600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr14:65031000-65039000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr14:65033400-65040000	Weak transcription	Gastric	stomach
7	chr14:65033600-65039200	Weak transcription	Aorta	Aorta
8	chr14:65033600-65039400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr14:65033800-65039400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr14:65033800-65039400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr14:65033800-65039400	Weak transcription	Brain Angular Gyrus	brain
12	chr14:65033800-65040000	Weak transcription	Esophagus	oesophagus
13	chr14:65034000-65039000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr14:65034400-65039200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr14:65034800-65039200	Weak transcription	Fetal Muscle Leg	muscle
16	chr14:65035000-65037600	Enhancers	Hela-S3	cervix
17	chr14:65035600-65037600	Enhancers	Brain Substantia Nigra	brain
18	chr14:65035800-65039400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr14:65036000-65041600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr14:65036200-65038600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr14:65036200-65038800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr14:65036200-65039400	Weak transcription	Adipose Nuclei	Adipose
23	chr14:65036200-65039400	Weak transcription	Brain Germinal Matrix	brain
24	chr14:65036200-65039600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr14:65036200-65039600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr14:65036200-65044000	Weak transcription	Fetal Kidney	kidney
27	chr14:65036400-65039000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr14:65036400-65039000	Weak transcription	Brain Anterior Caudate	brain
29	chr14:65036400-65039000	Weak transcription	Brain Hippocampus Middle	brain
30	chr14:65036400-65039000	Weak transcription	Colon Smooth Muscle	Colon
31	chr14:65036400-65039200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr14:65036400-65039200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr14:65036400-65039400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr14:65036400-65039400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr14:65036400-65039600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr14:65036600-65039000	Weak transcription	Fetal Lung	lung
37	chr14:65036600-65039400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr14:65036800-65039000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr14:65036800-65039200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr14:65037000-65039200	Weak transcription	A549	lung
41	chr14:65037000-65039400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr14:65037000-65039400	Weak transcription	Psoas Muscle	Psoas
43	chr14:65037000-65039400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr14:65037000-65039600	Weak transcription	HSMMtube	muscle
45	chr14:65037400-65039200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr14:65037400-65039400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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