Variant report

Variant	rs4639983
Chromosome Location	chr12:9104207-9104208
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr12:9101035-9104283	SK-N-SH	brain:	n/a	chr12:9102579-9102588

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:8850179..8851815-chr12:9101960..9104335,2	MCF-7	breast:
2	chr12:9103173..9107180-chr12:9112850..9116183,4	K562	blood:
3	chr12:9097804..9100498-chr12:9103089..9104894,4	K562	blood:
4	chr12:8849018..8850959-chr12:9102785..9104647,2	K562	blood:
5	chr12:9103372..9104890-chr12:9110140..9112943,2	MCF-7	breast:
6	chr12:9103173..9105935-chr12:9114683..9116241,2	K562	blood:
7	chr12:9096830..9100498-chr12:9102068..9104762,4	K562	blood:

No data

Variant related genes	Relation type
M6PR	TF binding region
ENSG00000166532	Chromatin interaction
ENSG00000003056	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10129061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10400516	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10400563	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs10743568	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10771238	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11048190	0.83[ASN][1000 genomes]
rs11048195	0.96[CHB][hapmap];0.83[ASN][1000 genomes]
rs11048264	0.81[ASN][1000 genomes]
rs11048337	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs11048338	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs11048344	0.82[ASN][1000 genomes]
rs11048345	0.82[ASN][1000 genomes]
rs1121401	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11614202	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12423746	0.82[ASN][1000 genomes]
rs12423817	0.82[ASN][1000 genomes]
rs12424026	0.82[ASN][1000 genomes]
rs12812913	0.82[ASN][1000 genomes]
rs12821842	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs12823100	0.96[CHB][hapmap];0.82[ASN][1000 genomes]
rs12833375	0.82[ASN][1000 genomes]
rs1476911	0.91[CHB][hapmap]
rs1805248	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1805724	0.96[CHB][hapmap];0.83[ASN][1000 genomes]
rs1805725	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1805727	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1805732	0.91[CHB][hapmap]
rs1805733	0.91[CHB][hapmap]
rs1805735	0.92[CEU][hapmap];0.96[CHB][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1805754	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1805761	0.95[CHB][hapmap]
rs1805765	0.82[CHB][hapmap]
rs2041624	0.82[ASN][1000 genomes]
rs2041625	0.82[ASN][1000 genomes]
rs2284349	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs2377671	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2377672	0.82[ASN][1000 genomes]
rs2377673	0.82[ASN][1000 genomes]
rs2377674	0.82[ASN][1000 genomes]
rs2377676	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34798934	0.82[ASN][1000 genomes]
rs4309200	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs4883201	0.85[CEU][hapmap]
rs4883203	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6832	0.95[CHB][hapmap]
rs7132930	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7300767	0.82[ASN][1000 genomes]
rs7301381	0.80[ASN][1000 genomes]
rs7309772	0.80[AFR][1000 genomes]
rs7957321	0.82[ASN][1000 genomes]
rs7961355	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7974486	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs887782	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs933462	0.96[CHB][hapmap];0.83[ASN][1000 genomes]
rs987917	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[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
rs4639983	M6PR	cis	lung	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9101000-9104400	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr12:9101800-9104600	Active TSS	Rectal Smooth Muscle	rectum
3	chr12:9102800-9105000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
4	chr12:9103000-9109400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:9103200-9104800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr12:9103200-9105400	Weak transcription	Gastric	stomach
7	chr12:9103400-9104600	Flanking Active TSS	Dnd41	blood
8	chr12:9103400-9105600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:9103400-9112000	Weak transcription	Pancreas	Pancrea
10	chr12:9103400-9116400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:9103600-9104600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
12	chr12:9103600-9104800	Enhancers	Small Intestine	intestine
13	chr12:9103600-9105000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr12:9103600-9105000	Enhancers	Primary B cells from peripheral blood	blood
15	chr12:9103600-9105200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:9103600-9105200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:9103600-9105400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:9103600-9105400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:9103600-9105600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:9103600-9105600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:9103600-9105600	Weak transcription	Brain Hippocampus Middle	brain
22	chr12:9103600-9105600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr12:9103600-9105600	Weak transcription	Fetal Intestine Small	intestine
24	chr12:9103600-9105800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:9103600-9110400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:9103600-9114000	Weak transcription	Fetal Kidney	kidney
27	chr12:9103600-9114200	Weak transcription	Aorta	Aorta
28	chr12:9103600-9114400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:9103600-9114600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:9103800-9104600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr12:9103800-9104600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:9103800-9104600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:9103800-9104800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr12:9103800-9104800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:9103800-9105000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr12:9103800-9105200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr12:9103800-9105400	Weak transcription	Liver	Liver
38	chr12:9103800-9105800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:9103800-9107200	Flanking Active TSS	Primary T cells from cord blood	blood
40	chr12:9104000-9104400	Flanking Active TSS	GM12878-XiMat	blood
41	chr12:9104000-9104400	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr12:9104000-9104600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:9104000-9104600	Enhancers	Fetal Thymus	thymus
44	chr12:9104000-9104600	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr12:9104000-9104800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr12:9104000-9104800	Enhancers	Adipose Nuclei	Adipose
47	chr12:9104000-9105000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:9104000-9105000	Enhancers	Thymus	Thymus
49	chr12:9104000-9105400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:9104000-9105600	Weak transcription	Left Ventricle	heart

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