Variant report

Variant	rs59869286
Chromosome Location	chr3:52779088-52779089
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11510435	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12107484	1.00[EUR][1000 genomes]
rs17052357	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17052404	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1963813	0.92[AFR][1000 genomes]
rs34173244	1.00[EUR][1000 genomes]
rs4532127	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56134416	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56156188	1.00[EUR][1000 genomes]
rs56276589	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56665533	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57008939	1.00[EUR][1000 genomes]
rs57298447	1.00[EUR][1000 genomes]
rs57560655	1.00[ASN][1000 genomes]
rs57757646	1.00[EUR][1000 genomes]
rs57789542	1.00[EUR][1000 genomes]
rs57869735	1.00[EUR][1000 genomes]
rs57946083	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58409398	1.00[EUR][1000 genomes]
rs58528592	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58564212	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59638016	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60040519	1.00[EUR][1000 genomes]
rs60058353	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60256157	1.00[EUR][1000 genomes]
rs60311166	1.00[EUR][1000 genomes]
rs60770874	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60830326	1.00[EUR][1000 genomes]
rs61220667	1.00[EUR][1000 genomes]
rs61538294	1.00[EUR][1000 genomes]
rs6445536	1.00[EUR][1000 genomes]
rs6762788	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6769720	1.00[EUR][1000 genomes]
rs6780005	0.87[EUR][1000 genomes]
rs6780397	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6803492	0.83[AFR][1000 genomes]
rs72950424	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72950432	1.00[EUR][1000 genomes]
rs72950437	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960212	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960237	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960240	1.00[EUR][1000 genomes]
rs72960260	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960274	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960281	1.00[EUR][1000 genomes]
rs72960285	1.00[EUR][1000 genomes]
rs72965177	1.00[EUR][1000 genomes]
rs72965181	1.00[EUR][1000 genomes]
rs73839126	1.00[EUR][1000 genomes]
rs73839129	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7645785	1.00[EUR][1000 genomes]
rs764636	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7647992	1.00[EUR][1000 genomes]
rs934839	0.84[AFR][1000 genomes];1.00[EUR][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	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv508219	chr3:52741193-52803899	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
4	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52741600-52804000	Weak transcription	Psoas Muscle	Psoas
2	chr3:52749200-52779800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:52761600-52781000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:52761600-52802400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:52762000-52787000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:52763800-52788400	Strong transcription	Fetal Brain Female	brain
7	chr3:52763800-52802600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:52764000-52800200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:52764000-52802800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:52764400-52802600	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:52764800-52781600	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr3:52764800-52789400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:52765200-52789400	Strong transcription	Adipose Nuclei	Adipose
14	chr3:52765200-52793400	Strong transcription	Fetal Intestine Large	intestine
15	chr3:52765400-52800400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:52765600-52788800	Strong transcription	Brain Anterior Caudate	brain
17	chr3:52765600-52789000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:52765600-52789400	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr3:52766200-52789600	Strong transcription	Placenta	Placenta
20	chr3:52766400-52789400	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr3:52766400-52802600	Strong transcription	Fetal Thymus	thymus
22	chr3:52767000-52785400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr3:52767200-52788000	Strong transcription	Brain Germinal Matrix	brain
24	chr3:52767600-52802600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:52767600-52803400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr3:52767800-52779800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:52767800-52780200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr3:52767800-52786000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:52767800-52793000	Weak transcription	Small Intestine	intestine
30	chr3:52767800-52800600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:52768000-52785800	Weak transcription	Fetal Heart	heart
32	chr3:52768000-52785800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr3:52768000-52789800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:52768000-52803600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr3:52768200-52785800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:52768400-52779800	Weak transcription	Gastric	stomach
37	chr3:52768400-52797200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:52768800-52786600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:52768800-52803000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:52769600-52786200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:52770000-52786000	Weak transcription	Stomach Mucosa	stomach
42	chr3:52770200-52789000	Strong transcription	Fetal Stomach	stomach
43	chr3:52770200-52797200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:52770800-52789400	Strong transcription	Fetal Muscle Leg	muscle
45	chr3:52771000-52783200	Strong transcription	Ovary	ovary
46	chr3:52771000-52788800	Strong transcription	Lung	lung
47	chr3:52771200-52788800	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:52771200-52789400	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr3:52771200-52800800	Strong transcription	Fetal Lung	lung
50	chr3:52771400-52788200	Strong transcription	Left Ventricle	heart

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