Variant report

Variant	rs4752983
Chromosome Location	chr11:47352138-47352139
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47196984..47198613-chr11:47350804..47352943,2	MCF-7	breast:
2	chr11:47291226..47293092-chr11:47352052..47354178,2	K562	blood:
3	chr11:47350500..47353711-chr11:47353800..47358007,4	MCF-7	breast:
4	chr11:47351825..47352364-chr11:47376428..47377047,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149182	Chromatin interaction
ENSG00000110514	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1051006	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1052373	0.82[MEX][hapmap]
rs10769253	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10769254	0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10769255	0.91[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10838663	0.80[CEU][hapmap]
rs10838681	0.86[MEX][hapmap]
rs10838685	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10838686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10838687	0.88[ASW][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes]
rs10838689	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10838692	0.82[MEX][hapmap]
rs11039155	0.87[EUR][1000 genomes]
rs11039189	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11493249	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11530166	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs11821917	0.81[CEU][hapmap]
rs11824864	0.81[CEU][hapmap]
rs11828339	0.81[CEU][hapmap]
rs12222581	0.87[AMR][1000 genomes]
rs12574081	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12574410	0.80[CEU][hapmap]
rs1449626	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1449627	0.82[MEX][hapmap]
rs17198158	0.81[CEU][hapmap]
rs17790804	0.81[CEU][hapmap]
rs2242261	1.00[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap]
rs2242262	0.80[CEU][hapmap];0.86[YRI][hapmap]
rs2242511	0.89[CEU][hapmap]
rs2254240	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279238	1.00[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2290146	0.94[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290148	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305280	0.88[ASW][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap]
rs2306353	0.80[CEU][hapmap]
rs2957873	0.94[ASW][hapmap];0.82[MEX][hapmap]
rs3729802	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3729804	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3729805	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3781619	1.00[ASW][hapmap];0.80[CEU][hapmap];0.90[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap]
rs3824866	0.80[CEU][hapmap];0.96[YRI][hapmap]
rs3847503	0.81[CEU][hapmap]
rs4752839	0.81[CEU][hapmap]
rs4752965	0.80[CEU][hapmap]
rs4752973	0.94[ASW][hapmap];1.00[MEX][hapmap]
rs4752977	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4752978	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4752979	0.95[AMR][1000 genomes]
rs58023804	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59567949	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6485751	0.95[AMR][1000 genomes]
rs7118396	1.00[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap]
rs7120118	0.82[MEX][hapmap]
rs7120158	0.86[YRI][hapmap]
rs7124958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7395496	0.80[CEU][hapmap];0.89[YRI][hapmap]
rs753812	0.90[CEU][hapmap]
rs753992	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs753993	0.87[CHB][hapmap];0.89[AMR][1000 genomes]
rs7928073	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs830084	0.92[YRI][hapmap]
rs830085	0.82[MEX][hapmap]
rs9666924	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4752983	PTPMT1	cis	parietal	SCAN
rs4752983	DDB2	cis	lymphoblastoid	seeQTL
rs4752983	DDB2	Cis_1M	lymphoblastoid	RTeQTL
rs4752983	ACP2	cis	lymphoblastoid	seeQTL
rs4752983	ACP2	cis	multi-tissue	Pritchard
rs4752983	ACP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47294600-47355200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr11:47295400-47352600	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr11:47295800-47352800	Strong transcription	Duodenum Mucosa	Duodenum
4	chr11:47296000-47353600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr11:47323400-47352400	Strong transcription	Thymus	Thymus
6	chr11:47324200-47354600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr11:47324800-47352600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr11:47325000-47352400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr11:47325000-47352800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr11:47325400-47353000	Strong transcription	Fetal Intestine Small	intestine
11	chr11:47326000-47353600	Strong transcription	Fetal Stomach	stomach
12	chr11:47327800-47352200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:47338800-47356200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:47339200-47353000	Weak transcription	NH-A	brain
15	chr11:47340200-47352800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr11:47342200-47352400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr11:47342200-47353200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:47342400-47352400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr11:47342400-47352600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:47342600-47352200	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr11:47342600-47352200	Strong transcription	Fetal Brain Female	brain
22	chr11:47342600-47352400	Strong transcription	Dnd41	blood
23	chr11:47342600-47352600	Strong transcription	Liver	Liver
24	chr11:47342600-47352600	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr11:47342600-47352600	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr11:47342600-47353200	Strong transcription	Placenta	Placenta
27	chr11:47342800-47352200	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr11:47342800-47352400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr11:47342800-47352400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr11:47342800-47352400	Strong transcription	Ovary	ovary
31	chr11:47342800-47352400	Strong transcription	Pancreas	Pancrea
32	chr11:47342800-47352400	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr11:47342800-47352600	Strong transcription	Brain Germinal Matrix	brain
34	chr11:47342800-47352800	Strong transcription	Brain Anterior Caudate	brain
35	chr11:47342800-47353000	Strong transcription	Fetal Intestine Large	intestine
36	chr11:47342800-47353600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr11:47343200-47352200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr11:47343200-47352400	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr11:47343200-47352800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr11:47343200-47370600	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr11:47343800-47352800	Weak transcription	Fetal Brain Male	brain
42	chr11:47344800-47352400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr11:47344800-47352600	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr11:47344800-47353000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr11:47345000-47352400	Strong transcription	Brain Substantia Nigra	brain
46	chr11:47345000-47352600	Strong transcription	NHLF	lung
47	chr11:47345000-47353000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr11:47345400-47352200	Strong transcription	Colonic Mucosa	Colon
49	chr11:47345800-47352400	Weak transcription	Fetal Kidney	kidney
50	chr11:47346200-47352400	Strong transcription	iPS-15b Cell Line	embryonic stem cell

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