Variant report

Variant	rs28535121
Chromosome Location	chr3:135892798-135892799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:135860291..135862678-chr3:135891863..135894559,2	MCF-7	breast:
2	chr3:135886209..135888091-chr3:135890757..135893050,2	K562	blood:
3	chr3:135885575..135887195-chr3:135890153..135893026,2	MCF-7	breast:
4	chr3:135892696..135894968-chr3:135897212..135899768,3	MCF-7	breast:
5	chr3:135890394..135895932-chr3:135912281..135916097,6	MCF-7	breast:
6	chr3:135881427..135883402-chr3:135892260..135894929,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10048942	0.95[CEU][hapmap]
rs10222451	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512990	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11720497	1.00[ASN][1000 genomes]
rs12330335	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695644	0.83[EUR][1000 genomes]
rs13068210	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13079205	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13081671	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13082532	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097248	0.81[CEU][hapmap]
rs13321220	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393786	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393787	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403763	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs28509770	0.87[AMR][1000 genomes]
rs28519617	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28669017	1.00[GIH][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34864445	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35320690	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35352346	0.95[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35837273	1.00[ASN][1000 genomes]
rs3905668	0.88[EUR][1000 genomes]
rs56398805	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439629	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67109185	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67589653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6767060	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769762	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775778	0.95[CEU][hapmap];0.84[MEX][hapmap]
rs6786582	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]
rs6790083	1.00[LWK][hapmap]
rs6792630	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6793835	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6799056	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6799320	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6799517	0.87[AMR][1000 genomes]
rs73222243	0.83[EUR][1000 genomes]
rs9653930	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9827662	0.89[CEU][hapmap]
rs9834966	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9837158	0.94[GIH][hapmap]
rs9844666	1.00[ASW][hapmap];0.94[GIH][hapmap];0.81[TSI][hapmap]
rs9848926	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]
rs9870122	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9881400	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28535121	PPP2R3A	cis	cerebellum	SCAN
rs28535121	MSL2	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135862000-135904800	Weak transcription	Hela-S3	cervix
2	chr3:135870800-135895200	Weak transcription	Fetal Intestine Small	intestine
3	chr3:135871000-135897600	Weak transcription	Aorta	Aorta
4	chr3:135871200-135905000	Weak transcription	Fetal Stomach	stomach
5	chr3:135872800-135903600	Weak transcription	Thymus	Thymus
6	chr3:135874800-135897600	Weak transcription	Gastric	stomach
7	chr3:135880000-135906600	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr3:135882800-135893000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:135882800-135905200	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:135883400-135901800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:135883800-135901200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:135885600-135897800	Weak transcription	Fetal Thymus	thymus
13	chr3:135885800-135893400	Weak transcription	Ovary	ovary
14	chr3:135888800-135899400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr3:135889200-135905000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:135889400-135893800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:135889400-135901000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr3:135889400-135907000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr3:135889400-135910400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr3:135889600-135893600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr3:135889600-135893800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr3:135889600-135894600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:135889800-135894000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:135889800-135905000	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr3:135890000-135893600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:135890000-135903800	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr3:135890200-135893000	Enhancers	Right Atrium	heart
28	chr3:135890200-135894600	Enhancers	Primary B cells from peripheral blood	blood
29	chr3:135890400-135892800	Genic enhancers	Primary T cells from cord blood	blood
30	chr3:135890400-135893000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:135890400-135893200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:135890400-135893200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:135890400-135893600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:135890400-135897800	Weak transcription	Dnd41	blood
35	chr3:135890400-135898600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:135890400-135905000	Weak transcription	NHDF-Ad	bronchial
37	chr3:135890400-135909600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:135890600-135893200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:135890800-135892800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr3:135890800-135892800	Weak transcription	Osteobl	bone
41	chr3:135890800-135893000	Weak transcription	Brain Angular Gyrus	brain
42	chr3:135890800-135893200	Weak transcription	Brain Hippocampus Middle	brain
43	chr3:135891000-135893800	Weak transcription	Esophagus	oesophagus
44	chr3:135891000-135893800	Weak transcription	Pancreas	Pancrea
45	chr3:135891000-135894200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:135891000-135894200	Weak transcription	Lung	lung
47	chr3:135891000-135895000	Weak transcription	Left Ventricle	heart
48	chr3:135891000-135897600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:135891000-135898200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:135891000-135901200	Weak transcription	Primary hematopoietic stem cells	blood

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