Variant report

Variant	rs17052269
Chromosome Location	chr3:52595417-52595418
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1344932	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs17052322	1.00[ASW][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17052355	1.00[ASW][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1971811	1.00[AMR][1000 genomes]
rs28758860	1.00[MEX][hapmap]
rs41415947	0.89[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs56815357	1.00[AMR][1000 genomes]
rs57401769	1.00[AMR][1000 genomes]
rs57440640	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58242587	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59078569	0.94[AFR][1000 genomes]
rs59410274	0.94[AFR][1000 genomes]
rs59789322	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60351358	1.00[AMR][1000 genomes]
rs60404983	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60832323	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61418167	0.94[AFR][1000 genomes]
rs61484330	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6803865	1.00[YRI][hapmap]
rs7616059	1.00[YRI][hapmap]
rs7630920	1.00[MEX][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17052269	SPCS1	cis	lymphoblastoid	seeQTL

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	chr3:52578800-52598200	Strong transcription	Primary B cells from cord blood	blood
15	chr3:52578800-52598800	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr3:52578800-52599600	Strong transcription	Fetal Muscle Trunk	muscle
17	chr3:52578800-52601400	Strong transcription	Primary B cells from peripheral blood	blood
18	chr3:52579000-52598600	Strong transcription	Thymus	Thymus
19	chr3:52579000-52599200	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr3:52579200-52598200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:52580400-52598400	Strong transcription	Duodenum Mucosa	Duodenum
22	chr3:52580600-52598400	Strong transcription	Primary T cells from cord blood	blood
23	chr3:52580600-52598600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:52580800-52598800	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr3:52581000-52598400	Strong transcription	HUVEC	blood vessel
26	chr3:52581000-52601000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:52582600-52596200	Strong transcription	GM12878-XiMat	blood
28	chr3:52583200-52600400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:52583200-52600800	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr3:52584200-52598600	Strong transcription	Fetal Lung	lung
31	chr3:52584600-52599000	Strong transcription	Primary hematopoietic stem cells	blood
32	chr3:52585800-52627400	Weak transcription	Fetal Heart	heart
33	chr3:52587000-52598200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:52587000-52602400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:52587200-52719200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:52587400-52595600	Weak transcription	HMEC	breast
37	chr3:52587600-52599200	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:52587800-52598800	Strong transcription	Brain Germinal Matrix	brain
39	chr3:52588000-52598400	Strong transcription	HepG2	liver
40	chr3:52588800-52595600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr3:52588800-52598600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:52589400-52599000	Strong transcription	Liver	Liver
43	chr3:52589600-52597200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr3:52589600-52611600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:52590600-52598400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr3:52590800-52598000	Strong transcription	Fetal Brain Female	brain
47	chr3:52590800-52598600	Strong transcription	Adipose Nuclei	Adipose
48	chr3:52591000-52598400	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr3:52591000-52598600	Strong transcription	NH-A	brain
50	chr3:52591000-52688000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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