Variant report

Variant	rs17052357
Chromosome Location	chr3:52668638-52668639
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52663645..52665220-chr3:52667243..52669253,2	K562	blood:
2	chr3:52651986..52653955-chr3:52666537..52669431,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10510759	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs11510435	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12107484	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17052404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1963813	0.88[AFR][1000 genomes]
rs2028220	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs34173244	1.00[EUR][1000 genomes]
rs4532127	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56134416	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56156188	1.00[EUR][1000 genomes]
rs56276589	1.00[EUR][1000 genomes]
rs56665533	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57008939	1.00[EUR][1000 genomes]
rs57298447	1.00[EUR][1000 genomes]
rs57757646	1.00[EUR][1000 genomes]
rs57789542	1.00[EUR][1000 genomes]
rs57869735	1.00[EUR][1000 genomes]
rs57946083	1.00[EUR][1000 genomes]
rs58409398	1.00[EUR][1000 genomes]
rs58528592	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58564212	1.00[EUR][1000 genomes]
rs59638016	1.00[EUR][1000 genomes]
rs59869286	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60040519	1.00[EUR][1000 genomes]
rs60058353	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60256157	1.00[EUR][1000 genomes]
rs60311166	1.00[EUR][1000 genomes]
rs60770874	0.88[AFR][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[CEU][hapmap];1.00[EUR][1000 genomes]
rs6762788	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6769720	1.00[EUR][1000 genomes]
rs6774097	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs6780005	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6780397	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6803492	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72947583	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs72947584	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs72950424	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72950432	1.00[EUR][1000 genomes]
rs72950437	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72960212	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72960237	1.00[EUR][1000 genomes]
rs72960240	1.00[EUR][1000 genomes]
rs72960260	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72960274	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	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7643568	1.00[ASW][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs7645785	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs764636	1.00[EUR][1000 genomes]
rs7647992	1.00[EUR][1000 genomes]
rs934839	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17052357	SPCS1	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 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	chr3:52636800-52703600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:52637200-52715800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:52639600-52670000	Strong transcription	Dnd41	blood
14	chr3:52640800-52684600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:52641000-52670800	Weak transcription	Stomach Mucosa	stomach
16	chr3:52642400-52671000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:52642400-52676400	Weak transcription	Small Intestine	intestine
18	chr3:52642600-52711200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:52643400-52691200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:52643600-52677200	Weak transcription	Fetal Heart	heart
21	chr3:52643800-52682800	Weak transcription	K562	blood
22	chr3:52649400-52668800	Strong transcription	Primary B cells from cord blood	blood
23	chr3:52649800-52669800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:52650000-52712200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr3:52652800-52672400	Weak transcription	Gastric	stomach
26	chr3:52652800-52673600	Weak transcription	Aorta	Aorta
27	chr3:52653000-52671400	Weak transcription	Spleen	Spleen
28	chr3:52654000-52669600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:52655200-52716400	Strong transcription	Fetal Thymus	thymus
30	chr3:52655400-52669200	Strong transcription	HSMM	muscle
31	chr3:52655600-52669400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:52655600-52680200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:52655600-52680200	Strong transcription	Fetal Muscle Leg	muscle
34	chr3:52655800-52684600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:52655800-52697600	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr3:52655800-52704000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:52656000-52683200	Strong transcription	Adipose Nuclei	Adipose
38	chr3:52656400-52669200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:52656400-52669400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:52656600-52669200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:52656600-52680200	Strong transcription	Fetal Muscle Trunk	muscle
42	chr3:52656600-52704600	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr3:52657000-52697200	Strong transcription	Liver	Liver
44	chr3:52657000-52697600	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:52657400-52669200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr3:52657400-52669400	Strong transcription	Fetal Intestine Large	intestine
47	chr3:52657800-52669800	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr3:52658000-52669200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:52658000-52702800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr3:52658200-52669200	Strong transcription	GM12878-XiMat	blood

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