Variant report

Variant	rs17052404
Chromosome Location	chr3:52776664-52776665
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52776114..52776854-chr3:53020723..53021564,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10510759	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs11510435	0.93[AFR][1000 genomes];0.89[AMR][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]
rs17052357	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	0.94[AFR][1000 genomes]
rs34173244	1.00[EUR][1000 genomes]
rs4532127	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687685	1.00[MEX][hapmap]
rs56134416	0.88[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	0.92[AFR][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[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58409398	1.00[EUR][1000 genomes]
rs58528592	0.94[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]
rs59869286	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60040519	1.00[EUR][1000 genomes]
rs60058353	1.00[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	0.97[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[CEU][hapmap];1.00[EUR][1000 genomes]
rs6762788	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6769720	1.00[EUR][1000 genomes]
rs6780005	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6780397	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6803492	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs72950424	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72950432	1.00[EUR][1000 genomes]
rs72950437	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960212	0.95[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	1.00[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	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7643568	1.00[ASW][hapmap];0.96[LWK][hapmap];0.96[YRI][hapmap]
rs7645785	1.00[EUR][1000 genomes]
rs764636	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7647992	1.00[EUR][1000 genomes]
rs934839	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17052404	SPCS1	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 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	chr3:52756200-52777400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:52761600-52781000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:52761600-52802400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:52762000-52787000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:52763800-52788400	Strong transcription	Fetal Brain Female	brain
8	chr3:52763800-52802600	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:52764000-52800200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:52764000-52802800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:52764400-52802600	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:52764800-52781600	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr3:52764800-52789400	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:52765200-52789400	Strong transcription	Adipose Nuclei	Adipose
15	chr3:52765200-52793400	Strong transcription	Fetal Intestine Large	intestine
16	chr3:52765400-52800400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:52765600-52788800	Strong transcription	Brain Anterior Caudate	brain
18	chr3:52765600-52789000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:52765600-52789400	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr3:52766200-52789600	Strong transcription	Placenta	Placenta
21	chr3:52766400-52789400	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr3:52766400-52802600	Strong transcription	Fetal Thymus	thymus
23	chr3:52767000-52785400	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr3:52767200-52788000	Strong transcription	Brain Germinal Matrix	brain
25	chr3:52767600-52802600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:52767600-52803400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:52767800-52777000	Strong transcription	Liver	Liver
28	chr3:52767800-52777200	Weak transcription	Esophagus	oesophagus
29	chr3:52767800-52777600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr3:52767800-52779800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:52767800-52780200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr3:52767800-52786000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:52767800-52793000	Weak transcription	Small Intestine	intestine
34	chr3:52767800-52800600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:52768000-52777200	Weak transcription	Right Ventricle	heart
36	chr3:52768000-52777400	Weak transcription	NHLF	lung
37	chr3:52768000-52777600	Weak transcription	Fetal Brain Male	brain
38	chr3:52768000-52785800	Weak transcription	Fetal Heart	heart
39	chr3:52768000-52785800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr3:52768000-52789800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:52768000-52803600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:52768200-52785800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:52768400-52779800	Weak transcription	Gastric	stomach
44	chr3:52768400-52797200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:52768800-52786600	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr3:52768800-52803000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:52769600-52786200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:52770000-52777600	Weak transcription	Hela-S3	cervix
49	chr3:52770000-52786000	Weak transcription	Stomach Mucosa	stomach
50	chr3:52770200-52777200	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links