Variant report

Variant	rs4521287
Chromosome Location	chr3:160812752-160812753
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	chr3:160809965..160812767-chr3:160891424..160893829,2	MCF-7	breast:
2	chr3:160811687..160814134-chr3:161129649..161132239,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10154889	0.85[CEU][hapmap];0.86[AMR][1000 genomes]
rs10433352	0.86[MEX][hapmap];0.87[AMR][1000 genomes]
rs11711152	0.90[CEU][hapmap]
rs11712713	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11715733	0.87[AMR][1000 genomes]
rs11717272	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11718966	0.90[CEU][hapmap]
rs11720263	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11915989	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11922957	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11922959	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12696112	0.84[AMR][1000 genomes]
rs12696113	0.84[AMR][1000 genomes]
rs13060601	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13060718	0.90[AMR][1000 genomes]
rs13061088	0.94[ASN][1000 genomes]
rs13062651	0.83[AMR][1000 genomes]
rs13071892	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13071999	0.90[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap]
rs13073059	0.90[CEU][hapmap]
rs13085336	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13098896	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13256	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13315565	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1345156	0.90[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap]
rs1374787	0.81[MEX][hapmap]
rs1447622	0.94[CEU][hapmap]
rs1562464	0.90[CEU][hapmap];0.88[GIH][hapmap];0.85[TSI][hapmap]
rs1599388	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16831796	0.82[MEX][hapmap];0.85[AMR][1000 genomes]
rs16831886	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1868105	0.90[CEU][hapmap]
rs2014810	0.87[AMR][1000 genomes]
rs2044571	0.90[CEU][hapmap]
rs2889390	0.81[JPT][hapmap]
rs34221255	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34630898	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35127376	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35914913	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4494975	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4679929	0.85[AMR][1000 genomes]
rs4856700	0.90[CEU][hapmap];0.85[CHB][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs57145341	0.85[AMR][1000 genomes]
rs6441338	0.94[CEU][hapmap]
rs6441362	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6772723	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6794882	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6806015	0.92[AMR][1000 genomes]
rs68166680	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73021215	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73023235	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7610432	0.87[AMR][1000 genomes]
rs7618924	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7624185	0.90[CEU][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7628389	0.86[MEX][hapmap];0.86[AMR][1000 genomes]
rs7641892	0.90[CEU][hapmap]
rs898677	0.86[MEX][hapmap];0.87[AMR][1000 genomes]
rs964533	0.90[CEU][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9812507	0.90[CEU][hapmap];0.90[AMR][1000 genomes]
rs9822435	0.90[CEU][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9832109	0.90[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes]
rs9844267	0.89[CEU][hapmap];0.90[GIH][hapmap]
rs9845943	0.90[CEU][hapmap];0.90[GIH][hapmap]
rs9857482	0.90[CEU][hapmap]
rs9857855	0.87[AMR][1000 genomes]
rs9860537	0.90[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs9862086	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9876142	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9880269	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9883566	1.00[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.90[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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv877704	chr3:160806859-160836006	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4521287	SPTSSB	cis	Thyroid	GTEx
rs4521287	PPM1L	cis	cerebellum	SCAN
rs4521287	B3GALNT1	cis	lymphoblastoid	seeQTL
rs4521287	SPTSSB	cis	Adipose Subcutaneous	GTEx
rs4521287	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL
rs4521287	B3GALT3	cis	multi-tissue	Pritchard
rs4521287	NMD3	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160780800-160821400	Weak transcription	Fetal Brain Male	brain
2	chr3:160781800-160822000	Weak transcription	Thymus	Thymus
3	chr3:160787000-160822000	Weak transcription	Primary T cells from cord blood	blood
4	chr3:160787200-160818800	Weak transcription	Brain Germinal Matrix	brain
5	chr3:160789600-160818800	Weak transcription	Esophagus	oesophagus
6	chr3:160796000-160817400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:160796200-160821800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:160797000-160822000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:160797600-160817200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:160798600-160821800	Weak transcription	Brain Angular Gyrus	brain
11	chr3:160799800-160821800	Weak transcription	NHLF	lung
12	chr3:160799800-160822000	Weak transcription	HMEC	breast
13	chr3:160800200-160818200	Weak transcription	Fetal Intestine Small	intestine
14	chr3:160800200-160820000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:160800400-160813400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:160800400-160817200	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:160800400-160818800	Weak transcription	Gastric	stomach
18	chr3:160800400-160822200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:160800400-160822400	Weak transcription	Spleen	Spleen
20	chr3:160801000-160821800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr3:160801200-160822000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:160801600-160816600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:160801600-160818800	Weak transcription	Placenta	Placenta
24	chr3:160801600-160821800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:160802600-160821400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:160802600-160822000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:160802600-160822400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:160802800-160822000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:160803400-160819200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:160803400-160822000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:160803800-160822000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:160804400-160816600	Weak transcription	Fetal Brain Female	brain
33	chr3:160804400-160818200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:160804400-160822000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:160804400-160822000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:160804600-160812800	Weak transcription	Aorta	Aorta
37	chr3:160804600-160813000	Weak transcription	Fetal Intestine Large	intestine
38	chr3:160804600-160816200	Weak transcription	Ovary	ovary
39	chr3:160804600-160816400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr3:160804600-160816600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr3:160804600-160817200	Weak transcription	Brain Anterior Caudate	brain
42	chr3:160804600-160820400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:160804600-160821800	Weak transcription	Brain Substantia Nigra	brain
44	chr3:160804600-160821800	Weak transcription	HUVEC	blood vessel
45	chr3:160804600-160822200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:160804800-160815400	Weak transcription	Left Ventricle	heart
47	chr3:160805800-160815400	Weak transcription	Right Ventricle	heart
48	chr3:160805800-160818800	Weak transcription	Lung	lung
49	chr3:160806600-160815200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr3:160806600-160816800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links