Variant report

Variant	rs9866235
Chromosome Location	chr3:135749165-135749166
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12633805	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs13065499	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs13069408	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs13072433	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs13072690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13072782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13078865	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs13084404	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs13092707	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs13097172	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];0.98[TSI][hapmap]
rs1523593	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs1523599	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs1523600	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs16843611	0.94[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs2140450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs2177407	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs3946444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4075999	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs4678432	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs4678434	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs4678435	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs6439605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap]
rs6439610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6439622	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6439623	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs6439624	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs6779903	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs6803786	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs7625177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs7650079	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs940229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9682712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9846554	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap]
rs9852009	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs9852169	0.91[ASW][hapmap];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[MKK][hapmap];0.98[TSI][hapmap]
rs9856799	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9868239	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
rs9866235	ZBTB38	cis	cerebellum	SCAN
rs9866235	PCCB	cis	parietal	SCAN
rs9866235	PPP2R3A	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135718000-135753000	Weak transcription	Fetal Kidney	kidney
2	chr3:135721800-135763600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr3:135726400-135758400	Weak transcription	Lung	lung
4	chr3:135727400-135760600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:135727800-135769400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:135735800-135760600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:135738000-135750000	Weak transcription	Brain Substantia Nigra	brain
8	chr3:135738000-135758400	Weak transcription	Gastric	stomach
9	chr3:135738000-135761200	Weak transcription	Fetal Brain Male	brain
10	chr3:135738000-135775800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:135738200-135749600	Weak transcription	Brain Angular Gyrus	brain
12	chr3:135738400-135763600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:135738400-135763600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:135739800-135767800	Weak transcription	NHDF-Ad	bronchial
15	chr3:135741000-135763600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:135741800-135750000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:135741800-135759800	Weak transcription	Placenta	Placenta
18	chr3:135742000-135763200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:135742000-135763600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:135742200-135763600	Weak transcription	Fetal Intestine Small	intestine
21	chr3:135742200-135763600	Weak transcription	NHEK	skin
22	chr3:135742800-135774200	Weak transcription	HMEC	breast
23	chr3:135743000-135755600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:135744200-135763600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:135745000-135751200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:135745200-135750200	Weak transcription	Brain Anterior Caudate	brain
27	chr3:135745600-135750000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:135745600-135751200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:135745800-135750000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:135745800-135755200	Weak transcription	Psoas Muscle	Psoas
31	chr3:135746000-135750600	Weak transcription	Liver	Liver
32	chr3:135746000-135750800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:135746200-135790000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:135746400-135749400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:135746400-135749800	Strong transcription	Ovary	ovary
36	chr3:135746400-135763600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr3:135746600-135749200	Strong transcription	Left Ventricle	heart
38	chr3:135746600-135761000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:135746800-135749400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:135746800-135750200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:135747000-135749400	Weak transcription	Spleen	Spleen
42	chr3:135747000-135749600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:135747000-135749800	Weak transcription	Fetal Brain Female	brain
44	chr3:135747000-135757400	Weak transcription	Right Ventricle	heart
45	chr3:135747200-135750200	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:135747600-135756000	Weak transcription	HSMM	muscle
47	chr3:135747600-135760600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:135747800-135763600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:135748000-135750000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:135748400-135749800	Weak transcription	Brain Germinal Matrix	brain

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