Variant report

Variant	rs9828757
Chromosome Location	chr3:121639609-121639610
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11916150	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12695420	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13068522	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1474327	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1589700	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2091665	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2332056	0.82[AMR][1000 genomes]
rs2689276	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2700424	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34227248	0.82[AMR][1000 genomes]
rs3817599	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4419417	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6438689	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6770115	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6780559	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73181839	0.82[AMR][1000 genomes]
rs7626740	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7628167	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7638094	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7647751	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9289184	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9289185	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs953730	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9815649	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9829181	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9843053	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[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	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv877383	chr3:121465220-121650736	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv877384	chr3:121601577-121659774	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9828757	EAF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121592800-121646800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr3:121613800-121647200	Weak transcription	Left Ventricle	heart
3	chr3:121615800-121671600	Weak transcription	Pancreas	Pancrea
4	chr3:121616200-121659400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:121624000-121647800	Weak transcription	Adipose Nuclei	Adipose
6	chr3:121625000-121661200	Weak transcription	Thymus	Thymus
7	chr3:121625200-121640400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:121626200-121651600	Strong transcription	Primary B cells from peripheral blood	blood
9	chr3:121627400-121641600	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:121627400-121659200	Weak transcription	Lung	lung
11	chr3:121627400-121664600	Weak transcription	Aorta	Aorta
12	chr3:121627600-121645200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:121627600-121659200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:121628200-121659200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:121629800-121651400	Strong transcription	Primary B cells from cord blood	blood
16	chr3:121630200-121652200	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr3:121630400-121649600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr3:121631800-121664800	Weak transcription	Brain Angular Gyrus	brain
19	chr3:121633200-121661200	Weak transcription	Liver	Liver
20	chr3:121633400-121642800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:121633400-121645200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:121633400-121646200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:121633600-121649000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:121633800-121661200	Weak transcription	Right Ventricle	heart
25	chr3:121634000-121651400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr3:121634000-121651600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr3:121634000-121660400	Weak transcription	Fetal Kidney	kidney
28	chr3:121634600-121646200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:121634600-121647000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:121634800-121649600	Weak transcription	Brain Anterior Caudate	brain
31	chr3:121634800-121667000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr3:121635000-121670600	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:121635200-121666800	Weak transcription	Brain Substantia Nigra	brain
34	chr3:121635400-121647800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:121635600-121640600	Weak transcription	Primary T cells from cord blood	blood
36	chr3:121636000-121643400	Weak transcription	Fetal Intestine Small	intestine
37	chr3:121636400-121645400	Strong transcription	Primary hematopoietic stem cells	blood
38	chr3:121636800-121644000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:121638200-121640200	Weak transcription	GM12878-XiMat	blood
40	chr3:121638200-121645200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:121638400-121641000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:121638400-121664800	Weak transcription	Spleen	Spleen
43	chr3:121638600-121661000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:121638800-121640800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:121638800-121661000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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