Variant report

Variant	rs3794086
Chromosome Location	chr11:35329809-35329810
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:35325471..35328883-chr11:35329361..35332564,3	MCF-7	breast:
2	chr11:35325412..35330750-chr11:35411649..35414159,5	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1043101	0.92[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs10742340	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10742341	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10768122	0.92[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs10768123	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10768126	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10836360	1.00[CEU][hapmap];0.88[AMR][1000 genomes]
rs10836361	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10836362	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10836363	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10836364	0.92[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10836367	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10836369	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11033048	0.92[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11524863	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12273644	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs12361171	0.91[CEU][hapmap]
rs12796856	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1570214	0.92[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1570215	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17378105	0.92[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3088168	0.92[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs3763888	0.92[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3794089	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3794090	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3794091	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3794098	0.92[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3794099	0.92[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3794100	0.92[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3794101	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3794102	0.92[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3794103	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3847604	0.95[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4755394	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4755395	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4756203	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4756204	0.92[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4756205	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4756206	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57339940	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6484778	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7105505	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7105690	0.92[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7121587	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7946149	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv832120	chr11:35277410-35490304	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv2758264	chr11:35319320-35480522	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2759819	chr11:35319320-35480522	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3794086	PRRG4	cis	cerebellum	SCAN
rs3794086	HIPK3	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35324000-35336200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr11:35324400-35343200	Weak transcription	Gastric	stomach
3	chr11:35325200-35339000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr11:35325600-35339200	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr11:35327000-35333400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr11:35327000-35343400	Weak transcription	Fetal Lung	lung
7	chr11:35327200-35340600	Weak transcription	Brain Substantia Nigra	brain
8	chr11:35327400-35339000	Weak transcription	Aorta	Aorta
9	chr11:35327600-35330800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr11:35327600-35335200	Weak transcription	Esophagus	oesophagus
11	chr11:35327600-35336600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr11:35327600-35337400	Weak transcription	NHDF-Ad	bronchial
13	chr11:35327800-35330800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr11:35327800-35332200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr11:35327800-35333000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr11:35327800-35333200	Weak transcription	GM12878-XiMat	blood
17	chr11:35327800-35334800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr11:35327800-35334800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr11:35327800-35334800	Weak transcription	Pancreas	Pancrea
20	chr11:35327800-35335000	Weak transcription	Brain Germinal Matrix	brain
21	chr11:35327800-35335200	Weak transcription	Left Ventricle	heart
22	chr11:35327800-35335200	Weak transcription	Spleen	Spleen
23	chr11:35327800-35340400	Weak transcription	Brain Hippocampus Middle	brain
24	chr11:35327800-35340800	Weak transcription	NHLF	lung
25	chr11:35328800-35330200	Genic enhancers	Fetal Brain Female	brain
26	chr11:35329000-35334000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr11:35329200-35330600	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr11:35329400-35330000	Genic enhancers	Fetal Brain Male	brain
29	chr11:35329400-35330000	Weak transcription	HepG2	liver
30	chr11:35329400-35330200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr11:35329400-35334800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr11:35329600-35331400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr11:35329600-35333200	Weak transcription	Primary B cells from cord blood	blood
34	chr11:35329600-35335000	Weak transcription	Brain Anterior Caudate	brain
35	chr11:35329600-35335200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr11:35329600-35335200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr11:35329600-35340800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr11:35329800-35330200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr11:35329800-35330400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr11:35329800-35331800	Weak transcription	Placenta	Placenta
41	chr11:35329800-35333600	Weak transcription	Liver	Liver
42	chr11:35329800-35334800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr11:35329800-35340600	Weak transcription	Brain Angular Gyrus	brain

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