Variant report

Variant	rs2332389
Chromosome Location	chr14:70963019-70963020
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12232170	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12436902	0.88[EUR][1000 genomes]
rs12586325	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12586328	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17107997	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17108107	0.88[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]
rs17108176	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1953798	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1953802	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1959483	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1959484	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1959485	0.80[CHD][hapmap]
rs1959486	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2095807	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2293877	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28641689	0.82[ASN][1000 genomes]
rs34512695	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4143920	0.94[ASW][hapmap];0.86[CHB][hapmap];0.96[GIH][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap]
rs4899354	0.80[CHD][hapmap]
rs4902817	0.88[CEU][hapmap];0.86[CHB][hapmap];0.96[YRI][hapmap]
rs4902827	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56778245	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56824265	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57146008	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61671382	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7143655	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7145265	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7152771	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7154884	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7159432	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73293909	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73293935	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8014252	1.00[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes]
rs8014338	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8015163	0.88[EUR][1000 genomes]
rs8017584	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8021308	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv565042	chr14:70951234-71011734	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1050615	chr14:70954149-71013235	Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv2763072	chr14:70954149-71013247	Strong transcription ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2332389	PLEKHH1	cis	parietal	SCAN
rs2332389	MED6	cis	parietal	SCAN
rs2332389	MAP3K9	cis	cerebellum	SCAN
rs2332389	MED6	cis	cerebellum	SCAN
rs2332389	SLC8A3	cis	cerebellum	SCAN
rs2332389	ADAM20	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70955600-70965600	Weak transcription	Right Ventricle	heart
2	chr14:70956600-70966600	Weak transcription	Left Ventricle	heart
3	chr14:70957600-70963200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr14:70958600-70963200	Weak transcription	Aorta	Aorta
5	chr14:70958600-70963200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr14:70958600-70963200	Weak transcription	Lung	lung
7	chr14:70958600-70963200	Weak transcription	Ovary	ovary
8	chr14:70958600-70963800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr14:70958600-70964000	Weak transcription	Gastric	stomach
10	chr14:70958600-70966600	Weak transcription	Brain Anterior Caudate	brain
11	chr14:70958600-70967200	Weak transcription	Brain Angular Gyrus	brain
12	chr14:70958600-70989000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr14:70958800-70963200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr14:70958800-70964800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr14:70958800-70993800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr14:70959200-70963800	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr14:70959200-70965400	Weak transcription	Brain Hippocampus Middle	brain
18	chr14:70959200-70965800	Weak transcription	Adipose Nuclei	Adipose
19	chr14:70959600-70965000	Weak transcription	Colon Smooth Muscle	Colon
20	chr14:70960000-70964600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr14:70961000-70964400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr14:70962200-70964200	Strong transcription	Liver	Liver
23	chr14:70962400-70965000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr14:70962600-70963200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr14:70962800-70963200	Weak transcription	Pancreas	Pancrea

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