Variant report

Variant	rs6786582
Chromosome Location	chr3:135898984-135898985
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:135897079..135899316-chr3:135913540..135917066,4	MCF-7	breast:
2	chr3:135898599..135901770-chr3:135904262..135906651,3	K562	blood:
3	chr3:135897266..135900078-chr3:135915939..135918038,2	K562	blood:
4	chr3:135897732..135900107-chr3:135913150..135915130,2	MCF-7	breast:
5	chr3:135886156..135888628-chr3:135897104..135900045,2	MCF-7	breast:
6	chr3:135892696..135894968-chr3:135897212..135899768,3	MCF-7	breast:
7	chr3:135897191..135900047-chr3:135906521..135908665,2	MCF-7	breast:
8	chr3:135898194..135901174-chr3:135905151..135906839,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10048942	0.95[CEU][hapmap]
rs10222451	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512990	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11720497	1.00[ASN][1000 genomes]
rs12330335	1.00[CEU][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695644	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13068210	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13079205	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13081671	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13082532	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097248	0.81[CEU][hapmap]
rs13321220	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393786	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393787	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403763	1.00[CEU][hapmap]
rs28519617	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535121	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28669017	1.00[GIH][hapmap];0.95[LWK][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34324561	0.82[AFR][1000 genomes]
rs34864445	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35320690	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35352346	0.95[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35837273	1.00[ASN][1000 genomes]
rs3905668	0.89[EUR][1000 genomes]
rs56398805	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439629	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67109185	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67589653	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6767060	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769762	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775778	0.95[CEU][hapmap];0.84[MEX][hapmap]
rs6792630	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6793835	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6799056	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6799320	0.90[CEU][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73222243	0.83[EUR][1000 genomes]
rs9653930	1.00[CEU][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9826454	0.90[AFR][1000 genomes]
rs9827662	0.89[CEU][hapmap]
rs9832813	0.81[LWK][hapmap];0.81[MKK][hapmap]
rs9834966	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9837158	0.94[GIH][hapmap];1.00[YRI][hapmap]
rs9844666	0.94[GIH][hapmap]
rs9848926	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]
rs9870122	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9881400	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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
rs6786582	PPP2R3A	cis	cerebellum	SCAN
rs6786582	RNF184	cis	multi-tissue	Pritchard
rs6786582	MSL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135862000-135904800	Weak transcription	Hela-S3	cervix
2	chr3:135871200-135905000	Weak transcription	Fetal Stomach	stomach
3	chr3:135872800-135903600	Weak transcription	Thymus	Thymus
4	chr3:135880000-135906600	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr3:135882800-135905200	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:135883400-135901800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:135883800-135901200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:135888800-135899400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr3:135889200-135905000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:135889400-135901000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr3:135889400-135907000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr3:135889400-135910400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr3:135889800-135905000	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr3:135890000-135903800	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr3:135890400-135905000	Weak transcription	NHDF-Ad	bronchial
16	chr3:135890400-135909600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:135891000-135901200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:135891000-135901200	Weak transcription	NH-A	brain
19	chr3:135891000-135905000	Weak transcription	Brain Substantia Nigra	brain
20	chr3:135891400-135904200	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr3:135892800-135900400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:135892800-135901200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:135893000-135900000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:135893400-135901000	Weak transcription	HepG2	liver
25	chr3:135893600-135899800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr3:135893600-135900200	Weak transcription	HMEC	breast
27	chr3:135893600-135901200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:135893600-135901200	Weak transcription	Brain Angular Gyrus	brain
29	chr3:135893600-135901200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:135893600-135904800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:135893600-135905000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:135893600-135910400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:135894400-135906800	Weak transcription	Esophagus	oesophagus
34	chr3:135894600-135899600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:135895400-135899600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:135895400-135907000	Weak transcription	Fetal Brain Male	brain
37	chr3:135895800-135901400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr3:135896000-135900400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr3:135896200-135901200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr3:135896400-135905200	Weak transcription	Fetal Intestine Small	intestine
41	chr3:135896800-135901600	Enhancers	Primary T cells from cord blood	blood
42	chr3:135897000-135900400	Weak transcription	Brain Hippocampus Middle	brain
43	chr3:135897000-135904800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr3:135897200-135899800	Weak transcription	Colon Smooth Muscle	Colon
45	chr3:135897400-135901000	Weak transcription	Brain Anterior Caudate	brain
46	chr3:135897400-135901000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:135897400-135907600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:135897400-135909800	Enhancers	Primary T cells fromperipheralblood	blood
49	chr3:135897600-135909000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:135897600-135911000	Enhancers	Primary B cells from peripheral blood	blood

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