Variant report

Variant	rs9868239
Chromosome Location	chr3:135688453-135688454
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs12630389	0.81[ASN][1000 genomes]
rs12632791	0.85[ASN][1000 genomes]
rs12633805	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12637541	0.83[ASN][1000 genomes]
rs13059064	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065499	0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs13069408	0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs13072433	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs13072690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075579	0.87[ASN][1000 genomes]
rs13078865	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13079037	0.83[EUR][1000 genomes]
rs13084404	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13092707	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs13097172	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13097176	0.95[ASN][1000 genomes]
rs13097267	0.88[ASN][1000 genomes]
rs13100235	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1523593	0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1523598	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1523599	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1523600	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs16843560	0.82[ASN][1000 genomes]
rs16843611	0.94[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2140450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177407	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2400649	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34447526	0.88[ASN][1000 genomes]
rs35097316	0.83[ASN][1000 genomes]
rs35532770	0.87[ASN][1000 genomes]
rs35946332	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35961065	0.85[ASN][1000 genomes]
rs3946444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075999	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs4331626	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4678224	0.86[ASN][1000 genomes]
rs4678288	0.88[ASN][1000 genomes]
rs4678432	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4678434	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4678435	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs55873361	0.88[ASN][1000 genomes]
rs56152207	0.88[ASN][1000 genomes]
rs57594457	0.88[ASN][1000 genomes]
rs60070757	0.88[ASN][1000 genomes]
rs61791712	0.88[ASN][1000 genomes]
rs61791714	0.88[ASN][1000 genomes]
rs6439603	0.82[ASN][1000 genomes]
rs6439605	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6439609	0.83[ASN][1000 genomes]
rs6439610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6439614	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6439615	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439618	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439622	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6439623	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6439624	0.94[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs6770366	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6771950	0.88[ASN][1000 genomes]
rs6775261	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779903	0.93[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs6793273	0.80[ASN][1000 genomes]
rs6803786	0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs7433592	0.88[ASN][1000 genomes]
rs7610302	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625177	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625607	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7635621	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650079	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9289501	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs940229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9682712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9758578	0.89[ASN][1000 genomes]
rs9846554	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9852009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9852169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9856799	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9866235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap]

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	nsv460860	chr3:135107678-135769006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv591829	chr3:135107678-135769006	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv829732	chr3:135561706-135756840	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9868239	PCCB	cis	cerebellum	SCAN
rs9868239	PPP2R3A	cis	cerebellum	SCAN
rs9868239	ZBTB38	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135685400-135692600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:135685600-135693800	Weak transcription	Gastric	stomach
3	chr3:135685800-135693800	Weak transcription	Lung	lung
4	chr3:135686000-135689000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:135686200-135689400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:135686400-135690000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:135686600-135690200	Enhancers	NHEK	skin
8	chr3:135686600-135690400	Enhancers	HMEC	breast
9	chr3:135686600-135693400	Weak transcription	Right Ventricle	heart
10	chr3:135686600-135694400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:135686800-135688800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr3:135686800-135689400	Weak transcription	Aorta	Aorta
13	chr3:135686800-135689400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:135686800-135692600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:135687000-135688800	Weak transcription	Brain Anterior Caudate	brain
16	chr3:135687000-135689200	Weak transcription	HSMMtube	muscle
17	chr3:135687000-135690800	Enhancers	NHDF-Ad	bronchial
18	chr3:135687000-135691000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:135687000-135691200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:135687000-135691800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr3:135687000-135692400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:135687000-135692800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:135687000-135692800	Weak transcription	Right Atrium	heart
24	chr3:135687000-135693200	Weak transcription	Fetal Lung	lung
25	chr3:135687000-135693200	Weak transcription	Fetal Stomach	stomach
26	chr3:135687200-135689400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:135687200-135690200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:135687200-135691400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:135687200-135691600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:135687200-135692600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:135687400-135688800	Weak transcription	Brain Angular Gyrus	brain
32	chr3:135687400-135689000	Weak transcription	Osteobl	bone
33	chr3:135687400-135689400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:135687400-135689400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr3:135687400-135690000	Enhancers	NHLF	lung
36	chr3:135687400-135690400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:135687400-135692800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr3:135687400-135692800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:135687400-135692800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr3:135687400-135693400	Weak transcription	Left Ventricle	heart
41	chr3:135687600-135688600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:135687600-135688600	Weak transcription	Psoas Muscle	Psoas
43	chr3:135687600-135688600	Enhancers	Rectal Smooth Muscle	rectum
44	chr3:135687600-135688800	Weak transcription	HSMM	muscle
45	chr3:135687600-135689000	Weak transcription	NH-A	brain
46	chr3:135687600-135689200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:135687600-135689400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:135687600-135689600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:135687600-135690400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:135687600-135690600	Weak transcription	Ovary	ovary

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