Variant report

Variant	rs1049457
Chromosome Location	chr2:87003028-87003029
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	chr2:86995678..86997239-chr2:87001923..87004036,2	K562	blood:
2	chr2:87002968..87006528-chr2:87006846..87010010,3	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10186663	0.83[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10201422	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1049458	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11547281	0.88[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs11889231	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1193	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12613610	0.81[CEU][hapmap]
rs12714203	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12997796	0.87[CHD][hapmap]
rs13029597	0.84[ASN][1000 genomes]
rs13297	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1850138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1878109	0.83[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2063848	0.83[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap]
rs2138396	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2138397	0.95[CEU][hapmap]
rs2271666	0.83[MEX][hapmap]
rs2367378	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2367379	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2887012	0.83[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34353387	0.87[CHD][hapmap]
rs35594332	0.87[CHD][hapmap]
rs36100635	0.90[CEU][hapmap]
rs4832049	0.88[MEX][hapmap]
rs4832311	0.95[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap]
rs4832312	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6547705	0.83[MEX][hapmap]
rs6705448	0.83[MEX][hapmap]
rs6706378	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711696	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711700	0.86[EUR][1000 genomes]
rs6726451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731890	0.83[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67535255	0.84[ASN][1000 genomes]
rs67856656	0.84[ASN][1000 genomes]
rs67864369	0.82[ASN][1000 genomes]
rs7561172	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7596943	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9309636	0.83[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9309637	0.83[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9309638	0.83[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs938486	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv10063	chr2:86940988-87084360	Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1002420	chr2:86948835-87172715	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv874472	chr2:86961252-87071474	Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1008817	chr2:86970406-87172715	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv14382	chr2:86972214-87174121	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv997982	chr2:86972834-87105864	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1007746	chr2:86972834-87172715	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv458585	chr2:86974318-87108211	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv582373	chr2:86974318-87108211	Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv1007307	chr2:86974563-87055214	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv535809	chr2:86974563-87055214	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv1003748	chr2:86975514-87032318	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
14	nsv535810	chr2:86975514-87032318	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
15	nsv1004572	chr2:86975514-87082883	Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
16	nsv535811	chr2:86975514-87082883	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1049457	PLGLB1	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86974200-87004200	Weak transcription	Small Intestine	intestine
2	chr2:86975800-87006600	Weak transcription	NH-A	brain
3	chr2:86981400-87004600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:86981600-87007000	Weak transcription	NHDF-Ad	bronchial
5	chr2:86984200-87006000	Weak transcription	Ovary	ovary
6	chr2:86984600-87007600	Weak transcription	Psoas Muscle	Psoas
7	chr2:86988800-87006200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:86991600-87004600	Strong transcription	Primary B cells from cord blood	blood
9	chr2:86991800-87004200	Strong transcription	Primary T cells from cord blood	blood
10	chr2:86991800-87004600	Genic enhancers	Fetal Thymus	thymus
11	chr2:86992000-87003400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:86992200-87003200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr2:86992200-87004400	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr2:86992200-87004400	Strong transcription	Dnd41	blood
15	chr2:86992200-87004600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:86992200-87004600	Strong transcription	Fetal Intestine Large	intestine
17	chr2:86992400-87003800	Strong transcription	Fetal Intestine Small	intestine
18	chr2:86992400-87004000	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr2:86992400-87004400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:86992400-87004600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:86992400-87004800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr2:86992600-87003200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:86992600-87003200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr2:86992600-87003400	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr2:86992600-87003800	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr2:86992600-87003800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:86992600-87004000	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr2:86992600-87004200	Strong transcription	Primary hematopoietic stem cells	blood
29	chr2:86992600-87004200	Strong transcription	Duodenum Mucosa	Duodenum
30	chr2:86992600-87004400	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr2:86992600-87004600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:86992800-87003800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:86992800-87003800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:86992800-87004000	Strong transcription	Liver	Liver
35	chr2:86993000-87003800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:86994600-87003400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:86994600-87004400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr2:86994600-87004400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr2:86994800-87004200	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:86995200-87003200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr2:86995200-87003200	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:86995400-87004000	Strong transcription	Esophagus	oesophagus
43	chr2:86995400-87004200	Strong transcription	GM12878-XiMat	blood
44	chr2:86995800-87004400	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:86996400-87004200	Strong transcription	Adipose Nuclei	Adipose
46	chr2:86996400-87004400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:86997000-87004000	Strong transcription	NHEK	skin
48	chr2:86997000-87004400	Strong transcription	Fetal Muscle Trunk	muscle
49	chr2:86997000-87004600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr2:86998200-87004600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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