Variant report

Variant	rs9848926
Chromosome Location	chr3:135816302-135816303
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr3:135816009-135816331	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
PPP2R3A	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10048942	0.95[CEU][hapmap]
rs10222451	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10512990	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12330335	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12695644	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13068210	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13079205	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081671	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13082532	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13097248	0.81[CEU][hapmap]
rs13321220	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1393786	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1393787	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1403763	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs28509770	0.82[EUR][1000 genomes]
rs28519617	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28535121	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28669017	0.97[GIH][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34864445	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35320690	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35352346	0.95[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3905668	0.80[EUR][1000 genomes]
rs56398805	0.80[EUR][1000 genomes]
rs6439629	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67109185	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67589653	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767060	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6769762	0.89[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6775778	0.95[CEU][hapmap];0.84[MEX][hapmap]
rs6786582	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6792630	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793835	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799056	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6799320	0.90[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799517	0.82[EUR][1000 genomes]
rs9653930	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827662	0.89[CEU][hapmap]
rs9834966	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9844666	0.91[GIH][hapmap]
rs9870122	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9881400	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][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	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
2	nsv4023	chr3:135772198-135816635	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9848926	PPP2R3A	cis	cerebellum	SCAN
rs9848926	MSL2	cis	cerebellum	SCAN
rs9848926	ZBTB38	cis	cerebellum	SCAN
rs9848926	RNF184	cis	multi-tissue	Pritchard

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135790200-135830800	Weak transcription	Psoas Muscle	Psoas
2	chr3:135803000-135826600	Weak transcription	Liver	Liver
3	chr3:135803400-135848000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:135803600-135821600	Weak transcription	Right Ventricle	heart
5	chr3:135803600-135860600	Weak transcription	Esophagus	oesophagus
6	chr3:135803800-135832400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:135803800-135860000	Weak transcription	NHLF	lung
8	chr3:135804000-135832000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:135804000-135833200	Weak transcription	HMEC	breast
10	chr3:135804200-135819400	Weak transcription	Colonic Mucosa	Colon
11	chr3:135804600-135822200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:135805200-135832000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:135805200-135832800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:135805400-135843800	Weak transcription	NHEK	skin
15	chr3:135807200-135822000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:135807400-135833200	Weak transcription	Lung	lung
17	chr3:135809200-135816400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:135810000-135828800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:135810200-135822200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:135810200-135822200	Weak transcription	Brain Anterior Caudate	brain
21	chr3:135810200-135825600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr3:135810200-135827800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:135810200-135832800	Weak transcription	Brain Angular Gyrus	brain
24	chr3:135810200-135835600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:135810200-135835800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:135810400-135819600	Weak transcription	HSMMtube	muscle
27	chr3:135810400-135820800	Weak transcription	Fetal Kidney	kidney
28	chr3:135810400-135820800	Weak transcription	Left Ventricle	heart
29	chr3:135810400-135820800	Weak transcription	Ovary	ovary
30	chr3:135810400-135821000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:135810400-135821400	Weak transcription	Fetal Brain Female	brain
32	chr3:135810400-135821600	Weak transcription	Adipose Nuclei	Adipose
33	chr3:135810400-135822000	Weak transcription	Brain Germinal Matrix	brain
34	chr3:135810400-135822000	Weak transcription	Fetal Intestine Large	intestine
35	chr3:135810400-135822200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:135810400-135822200	Weak transcription	Aorta	Aorta
37	chr3:135810400-135822200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr3:135810400-135824000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:135810400-135824200	Weak transcription	Pancreas	Pancrea
40	chr3:135810400-135827000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr3:135810400-135828800	Weak transcription	Brain Substantia Nigra	brain
42	chr3:135810400-135830800	Weak transcription	Fetal Brain Male	brain
43	chr3:135810400-135831200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:135810400-135832000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:135810400-135832000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr3:135810400-135832800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:135810400-135842200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:135810400-135843000	Weak transcription	Gastric	stomach
49	chr3:135810400-135848000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:135810400-135855400	Weak transcription	Osteobl	bone

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