Variant report

Variant	rs61538294
Chromosome Location	chr3:52659594-52659595
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10510759	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11510435	1.00[EUR][1000 genomes]
rs12107484	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17052357	1.00[EUR][1000 genomes]
rs17052404	1.00[EUR][1000 genomes]
rs1987234	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs34173244	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35920544	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4532127	1.00[EUR][1000 genomes]
rs56134416	1.00[EUR][1000 genomes]
rs56156188	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56259931	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs56276589	1.00[EUR][1000 genomes]
rs56665533	1.00[EUR][1000 genomes]
rs57008939	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57246324	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57298447	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57319306	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57560655	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57757646	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57789542	1.00[EUR][1000 genomes]
rs57869735	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57946083	1.00[EUR][1000 genomes]
rs58100002	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58409398	1.00[EUR][1000 genomes]
rs58528592	1.00[EUR][1000 genomes]
rs58564212	1.00[EUR][1000 genomes]
rs58725214	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58924550	0.81[AFR][1000 genomes]
rs59638016	1.00[EUR][1000 genomes]
rs59869286	1.00[EUR][1000 genomes]
rs60040519	1.00[EUR][1000 genomes]
rs60058353	1.00[EUR][1000 genomes]
rs60256157	1.00[EUR][1000 genomes]
rs60311166	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60415551	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60611300	0.85[AFR][1000 genomes]
rs60682984	0.85[AFR][1000 genomes]
rs60770874	1.00[EUR][1000 genomes]
rs60823713	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60830326	1.00[EUR][1000 genomes]
rs60916588	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61220667	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6445536	1.00[EUR][1000 genomes]
rs6762788	1.00[EUR][1000 genomes]
rs6769720	1.00[EUR][1000 genomes]
rs6780005	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6780397	1.00[EUR][1000 genomes]
rs72947535	0.80[AFR][1000 genomes]
rs72947580	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72947589	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72950424	1.00[EUR][1000 genomes]
rs72950430	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72950432	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72950437	1.00[EUR][1000 genomes]
rs72960212	1.00[EUR][1000 genomes]
rs72960237	1.00[EUR][1000 genomes]
rs72960240	1.00[EUR][1000 genomes]
rs72960260	1.00[EUR][1000 genomes]
rs72960274	1.00[EUR][1000 genomes]
rs72960281	1.00[EUR][1000 genomes]
rs72960285	1.00[EUR][1000 genomes]
rs72965177	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72965181	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73839126	1.00[EUR][1000 genomes]
rs73839129	1.00[EUR][1000 genomes]
rs7645785	1.00[EUR][1000 genomes]
rs764636	1.00[EUR][1000 genomes]
rs7647992	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7648016	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs934839	1.00[EUR][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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52587200-52719200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52591000-52688000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:52592200-52719200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:52634800-52686000	Strong transcription	Duodenum Mucosa	Duodenum
5	chr3:52636000-52703800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:52636000-52704000	Strong transcription	Placenta	Placenta
7	chr3:52636200-52703200	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr3:52636600-52669200	Strong transcription	Primary B cells from peripheral blood	blood
9	chr3:52636600-52673600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:52636600-52677400	Weak transcription	Pancreas	Pancrea
11	chr3:52636800-52662800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:52636800-52703600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr3:52637200-52715800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:52639600-52670000	Strong transcription	Dnd41	blood
15	chr3:52640600-52663200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:52640800-52684600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:52641000-52670800	Weak transcription	Stomach Mucosa	stomach
18	chr3:52641600-52664800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:52642400-52671000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:52642400-52676400	Weak transcription	Small Intestine	intestine
21	chr3:52642600-52711200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:52643400-52691200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:52643600-52677200	Weak transcription	Fetal Heart	heart
24	chr3:52643800-52660200	Weak transcription	Fetal Brain Male	brain
25	chr3:52643800-52682800	Weak transcription	K562	blood
26	chr3:52648400-52660400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:52649400-52668800	Strong transcription	Primary B cells from cord blood	blood
28	chr3:52649800-52669800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:52650000-52712200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr3:52650400-52660200	Weak transcription	Hela-S3	cervix
31	chr3:52650800-52661400	Weak transcription	Right Ventricle	heart
32	chr3:52651400-52662200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:52651400-52666400	Weak transcription	Fetal Intestine Small	intestine
34	chr3:52651800-52659600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr3:52652400-52660000	Strong transcription	Fetal Stomach	stomach
36	chr3:52652800-52672400	Weak transcription	Gastric	stomach
37	chr3:52652800-52673600	Weak transcription	Aorta	Aorta
38	chr3:52653000-52671400	Weak transcription	Spleen	Spleen
39	chr3:52654000-52667600	Weak transcription	Colonic Mucosa	Colon
40	chr3:52654000-52669600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:52654600-52659600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr3:52654800-52659800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:52654800-52660200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr3:52655200-52660000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:52655200-52716400	Strong transcription	Fetal Thymus	thymus
46	chr3:52655400-52669200	Strong transcription	HSMM	muscle
47	chr3:52655600-52660400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr3:52655600-52669400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:52655600-52680200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:52655600-52680200	Strong transcription	Fetal Muscle Leg	muscle

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