Variant report

Variant	rs1987234
Chromosome Location	chr3:52598359-52598360
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10510759	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12107484	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs34173244	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs35920544	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56156188	0.84[AFR][1000 genomes]
rs56259931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56960576	1.00[EUR][1000 genomes]
rs57008939	0.84[AFR][1000 genomes]
rs57246324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57298447	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57319306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57560655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57757646	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs57869735	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58100002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58725214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58924550	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60311166	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60415551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60611300	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60682984	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60823713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60916588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61220667	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61538294	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6445536	0.85[AMR][1000 genomes]
rs6780005	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72947535	0.96[AFR][1000 genomes]
rs72947580	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72947583	1.00[EUR][1000 genomes]
rs72947584	1.00[EUR][1000 genomes]
rs72947589	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72950430	0.85[AFR][1000 genomes]
rs72950432	0.83[AFR][1000 genomes]
rs72960240	0.85[AMR][1000 genomes]
rs72960281	0.85[AMR][1000 genomes]
rs72965177	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72965181	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73837804	1.00[EUR][1000 genomes]
rs7619643	0.85[AMR][1000 genomes]
rs7647992	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7648016	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv822092	chr3:52598226-52601851	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	2 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	chr3:52572400-52633000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:52573600-52598400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:52574400-52623800	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr3:52574600-52598800	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr3:52574800-52605000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:52576800-52625600	Strong transcription	Fetal Thymus	thymus
7	chr3:52577000-52599000	Strong transcription	Fetal Muscle Leg	muscle
8	chr3:52577200-52599000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:52577600-52598600	Strong transcription	Placenta	Placenta
10	chr3:52577600-52605200	Strong transcription	Dnd41	blood
11	chr3:52578200-52625600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr3:52578400-52598600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:52578400-52600600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:52578800-52598800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr3:52578800-52599600	Strong transcription	Fetal Muscle Trunk	muscle
16	chr3:52578800-52601400	Strong transcription	Primary B cells from peripheral blood	blood
17	chr3:52579000-52598600	Strong transcription	Thymus	Thymus
18	chr3:52579000-52599200	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:52580400-52598400	Strong transcription	Duodenum Mucosa	Duodenum
20	chr3:52580600-52598400	Strong transcription	Primary T cells from cord blood	blood
21	chr3:52580600-52598600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr3:52580800-52598800	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr3:52581000-52598400	Strong transcription	HUVEC	blood vessel
24	chr3:52581000-52601000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:52583200-52600400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:52583200-52600800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr3:52584200-52598600	Strong transcription	Fetal Lung	lung
28	chr3:52584600-52599000	Strong transcription	Primary hematopoietic stem cells	blood
29	chr3:52585800-52627400	Weak transcription	Fetal Heart	heart
30	chr3:52587000-52602400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:52587200-52719200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:52587600-52599200	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:52587800-52598800	Strong transcription	Brain Germinal Matrix	brain
34	chr3:52588000-52598400	Strong transcription	HepG2	liver
35	chr3:52588800-52598600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:52589400-52599000	Strong transcription	Liver	Liver
37	chr3:52589600-52611600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:52590600-52598400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:52590800-52598600	Strong transcription	Adipose Nuclei	Adipose
40	chr3:52591000-52598400	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr3:52591000-52598600	Strong transcription	NH-A	brain
42	chr3:52591000-52688000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr3:52591200-52598600	Strong transcription	HSMMtube	muscle
44	chr3:52591200-52599000	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr3:52591200-52601400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:52591400-52598400	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:52591400-52598800	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:52591400-52599200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:52591400-52599200	Strong transcription	Fetal Intestine Large	intestine
50	chr3:52591600-52598800	Strong transcription	HUES6 Cell Line	embryonic stem cell

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