Variant report

Variant	rs1805248
Chromosome Location	chr12:9101137-9101138
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:9101100-9103207	GM12891	blood:	n/a	n/a
2	POLR2A	chr12:9101049-9103146	MCF10A-Er-Src	breast:	n/a	n/a
3	IRF1	chr12:9100899-9103127	K562	blood:	n/a	chr12:9101236-9101248 chr12:9101237-9101247 chr12:9101235-9101255 chr12:9101237-9101251 chr12:9101236-9101248 chr12:9101367-9101376 chr12:9102370-9102379 chr12:9102242-9102262 chr12:9101236-9101250 chr12:9101111-9101120
4	EP300	chr12:9101091-9101242	K562	blood:	n/a	chr12:9101107-9101121
5	WRNIP1	chr12:9100991-9103253	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:9100911-9103002	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:9100949-9103269	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr12:9101114-9101757	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr12:9101063-9102924	IMR90	lung:	n/a	n/a
10	MXI1	chr12:9101035-9104283	SK-N-SH	brain:	n/a	chr12:9102579-9102588
11	MXI1	chr12:9101119-9103770	IMR90	lung:	n/a	chr12:9102579-9102588

No.	Distal block	Cell Line	Cell type
1	chr12:9064351..9068260-chr12:9100706..9102986,3	MCF-7	breast:
2	chr12:9086089..9087929-chr12:9099669..9102471,2	MCF-7	breast:
3	chr12:9065401..9068009-chr12:9098811..9103435,5	MCF-7	breast:
4	chr12:8831240..8834725-chr12:9101135..9103936,3	MCF-7	breast:
5	chr12:9066826..9070397-chr12:9099293..9102558,3	K562	blood:
6	chr12:9083802..9086315-chr12:9099049..9101665,2	MCF-7	breast:
7	chr12:9093100..9096905-chr12:9100746..9103868,4	K562	blood:
8	chr12:9081265..9083698-chr12:9100850..9103403,2	MCF-7	breast:
9	chr12:9100379..9103293-chr12:9215519..9218225,4	MCF-7	breast:

Variant related genes	Relation type
M6PR	TF binding region
KLRG1	TF binding region
ENSG00000111752	Chromatin interaction
ENSG00000245105	Chromatin interaction
ENSG00000214851	Chromatin interaction
ENSG00000003056	Chromatin interaction
ENSG00000256004	Chromatin interaction
ENSG00000166532	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10129061	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10400516	0.90[ASN][1000 genomes]
rs10400563	0.86[CHB][hapmap]
rs1049925	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs10743568	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10771238	0.87[ASN][1000 genomes]
rs10842660	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs11048190	0.89[ASN][1000 genomes]
rs11048195	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11048264	0.87[ASN][1000 genomes]
rs11048337	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs11048338	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs11048344	0.88[ASN][1000 genomes]
rs11048345	0.88[ASN][1000 genomes]
rs11048434	0.86[JPT][hapmap]
rs11494570	0.80[ASN][1000 genomes]
rs11614202	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12371786	0.86[ASN][1000 genomes]
rs12422905	0.83[ASN][1000 genomes]
rs12423746	0.88[ASN][1000 genomes]
rs12423817	0.88[ASN][1000 genomes]
rs12424026	0.88[ASN][1000 genomes]
rs12812913	0.88[ASN][1000 genomes]
rs12821842	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs12823100	0.95[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs12824212	0.86[JPT][hapmap]
rs12833375	0.88[ASN][1000 genomes]
rs1476911	0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1805677	0.86[JPT][hapmap]
rs1805719	0.87[JPT][hapmap]
rs1805721	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs1805722	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs1805723	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs1805724	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1805725	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1805727	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1805732	0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1805733	0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1805735	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs1805736	0.81[JPT][hapmap]
rs1805754	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1805761	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1805765	0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2041624	0.88[ASN][1000 genomes]
rs2041625	0.88[ASN][1000 genomes]
rs2080116	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs2159961	0.81[JPT][hapmap]
rs2284349	0.81[CHB][hapmap]
rs2377671	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2377672	0.87[ASN][1000 genomes]
rs2377673	0.88[ASN][1000 genomes]
rs2377674	0.88[ASN][1000 genomes]
rs34285491	0.80[ASN][1000 genomes]
rs34798934	0.88[ASN][1000 genomes]
rs4309200	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs4639983	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4883203	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6832	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7300767	0.88[ASN][1000 genomes]
rs7301381	0.86[ASN][1000 genomes]
rs7309922	0.85[ASN][1000 genomes]
rs7315055	0.84[ASN][1000 genomes]
rs7957321	0.88[ASN][1000 genomes]
rs7961355	0.87[ASN][1000 genomes]
rs887782	0.85[YRI][hapmap]
rs933462	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs987917	1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][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	nsv832327	chr12:9081779-9246220	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1805248	M6PR	cis	lung	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9087000-9101200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:9091600-9101200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:9096600-9101200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:9098000-9101400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:9098200-9101200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:9098200-9101200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:9098200-9101200	Weak transcription	Colonic Mucosa	Colon
8	chr12:9098200-9101200	Weak transcription	Gastric	stomach
9	chr12:9098200-9101200	Weak transcription	Pancreas	Pancrea
10	chr12:9098200-9101400	Weak transcription	Aorta	Aorta
11	chr12:9098200-9101400	Weak transcription	Esophagus	oesophagus
12	chr12:9098400-9101200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:9098400-9101200	Weak transcription	Ovary	ovary
14	chr12:9098400-9101400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:9098400-9101400	Weak transcription	Lung	lung
16	chr12:9098600-9101200	Weak transcription	Fetal Kidney	kidney
17	chr12:9099000-9101200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr12:9099000-9101200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr12:9099000-9101200	Weak transcription	Placenta	Placenta
20	chr12:9099200-9101200	Enhancers	Primary B cells from peripheral blood	blood
21	chr12:9099200-9101200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:9099200-9101200	Weak transcription	Left Ventricle	heart
23	chr12:9099400-9103600	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr12:9099600-9101200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr12:9099600-9101400	Enhancers	Small Intestine	intestine
26	chr12:9099600-9103600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:9099800-9101200	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr12:9100000-9101200	Enhancers	Stomach Mucosa	stomach
29	chr12:9100000-9101400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr12:9100000-9101800	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr12:9100200-9101200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr12:9100200-9101200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr12:9100200-9101200	Enhancers	Brain Germinal Matrix	brain
34	chr12:9100200-9101200	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr12:9100200-9101200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:9100200-9101400	Active TSS	Psoas Muscle	Psoas
37	chr12:9100200-9101400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr12:9100200-9101800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:9100200-9101800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:9100200-9103400	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr12:9100200-9103800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:9100200-9103800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:9100400-9101200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr12:9100400-9101200	Enhancers	Brain Angular Gyrus	brain
45	chr12:9100400-9101200	Flanking Active TSS	A549	lung
46	chr12:9100400-9101200	Flanking Active TSS	Hela-S3	cervix
47	chr12:9100400-9101200	Flanking Active TSS	HMEC	breast
48	chr12:9100400-9101400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:9100400-9101400	Flanking Active TSS	Dnd41	blood
50	chr12:9100400-9101600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links