Variant report

Variant	rs987917
Chromosome Location	chr12:9102575-9102576
allele	A/C
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	CCNT2	chr12:9101965-9102838	K562	blood:	n/a	n/a
2	MAX	chr12:9101328-9103384	GM12878	blood:	n/a	n/a
3	NFYA	chr12:9102166-9102822	K562	blood:	n/a	chr12:9102366-9102381 chr12:9102370-9102382 chr12:9102362-9102380 chr12:9102366-9102381 chr12:9102369-9102379 chr12:9102367-9102381 chr12:9102368-9102381
4	ELK4	chr12:9102021-9102806	HEK293	kidney:	n/a	chr12:9102245-9102256 chr12:9102246-9102255
5	JUN	chr12:9102426-9103017	H1-hESC	embryonic stem cell:	n/a	chr12:9102827-9102839
6	NRF1	chr12:9102175-9102640	H1-hESC	embryonic stem cell:	n/a	chr12:9102592-9102599
7	TBP	chr12:9101893-9103160	H1-hESC	embryonic stem cell:	n/a	n/a
8	ELF1	chr12:9101699-9103047	HCT-116	colon:	n/a	chr12:9102587-9102596 chr12:9102592-9102601
9	ZC3H11A	chr12:9102197-9103057	K562	blood:	n/a	n/a
10	EP300	chr12:9101847-9103097	GM12878	blood:	n/a	chr12:9102819-9102828
11	CTCF	chr12:9102574-9102853	Lung_OC	lung:	n/a	n/a
12	GABPA	chr12:9101866-9103159	HL-60	blood:	n/a	chr12:9102592-9102599
13	CTCF	chr12:9102561-9102840	A549	lung:	n/a	n/a
14	HEY1	chr12:9101871-9103006	K562	blood:	n/a	n/a
15	BRCA1	chr12:9102304-9103330	H1-hESC	embryonic stem cell:	n/a	n/a
16	CREB1	chr12:9101818-9102998	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:9101227-9102955	GM12892	blood:	n/a	n/a
18	POLR2A	chr12:9101199-9103047	GM12892	blood:	n/a	n/a
19	SMC3	chr12:9102342-9102954	K562	blood:	n/a	chr12:9102581-9102591
20	GABPA	chr12:9101794-9103073	MCF-7	breast:	n/a	chr12:9102592-9102599
21	TEAD4	chr12:9102000-9103154	K562	blood:	n/a	n/a
22	SRF	chr12:9102338-9102685	GM12878	blood:	n/a	n/a
23	GABPA	chr12:9101959-9103032	HL-60	blood:	n/a	chr12:9102592-9102599
24	MAX	chr12:9101838-9103154	A549	lung:	n/a	n/a
25	RAD21	chr12:9102441-9103090	A549	lung:	n/a	n/a
26	ETS1	chr12:9101894-9102852	GM12878	blood:	n/a	chr12:9102246-9102255 chr12:9102632-9102639 chr12:9102587-9102598 chr12:9102245-9102254 chr12:9102252-9102265 chr12:9102246-9102255 chr12:9102631-9102644 chr12:9102630-9102643 chr12:9102244-9102253 chr12:9102250-9102265
27	ELF1	chr12:9101712-9102939	GM12878	blood:	n/a	chr12:9102587-9102596 chr12:9102592-9102601
28	POLR2A	chr12:9101100-9103207	GM12891	blood:	n/a	n/a
29	MXI1	chr12:9101469-9103384	Hela-S3	cervix:	n/a	chr12:9102579-9102588
30	USF1	chr12:9101928-9102743	K562	blood:	n/a	n/a
31	TCF12	chr12:9101772-9103067	ECC-1	luminal epithelium:	n/a	chr12:9102578-9102588
32	POLR2A	chr12:9101212-9102938	GM12891	blood:	n/a	n/a
33	EBF1	chr12:9101913-9102630	GM12878	blood:	n/a	n/a
34	E2F6	chr12:9102084-9103096	A549	lung:	n/a	chr12:9102370-9102379 chr12:9102993-9103000
35	POLR2A	chr12:9101813-9102833	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr12:9101430-9103328	SK-N-MC	brain:	n/a	n/a
37	HEY1	chr12:9101868-9102984	HepG2	liver:	n/a	n/a
38	YY1	chr12:9102538-9102807	HCT-116	colon:	n/a	n/a
39	MYC	chr12:9101994-9103474	MCF10A-Er-Src	breast:	n/a	n/a
40	TAF1	chr12:9101829-9103029	ECC-1	luminal epithelium:	n/a	n/a
41	MAX	chr12:9102118-9103082	H1-hESC	embryonic stem cell:	n/a	n/a
42	PAX5	chr12:9102133-9102971	GM12878	blood:	n/a	n/a
43	POLR2A	chr12:9101712-9102873	MCF-7	breast:	n/a	n/a
44	POLR2A	chr12:9101847-9102959	HepG2	liver:	n/a	n/a
45	EP300	chr12:9102298-9102852	K562	blood:	n/a	chr12:9102819-9102828
46	USF1	chr12:9101911-9102770	A549	lung:	n/a	n/a
47	CTCF	chr12:9102080-9102966	GM12878	blood:	n/a	chr12:9102284-9102297
48	MYC	chr12:9101299-9103326	NB4	blood:	n/a	n/a
49	TAF1	chr12:9101796-9102865	SK-N-SH	brain:	n/a	n/a
50	NFYA	chr12:9102048-9103046	Hela-S3	cervix:	n/a	chr12:9102366-9102381 chr12:9102370-9102382 chr12:9102362-9102380 chr12:9102366-9102381 chr12:9102369-9102379 chr12:9102367-9102381 chr12:9102368-9102381

No.	Distal block	Cell Line	Cell type
1	chr12:8850179..8851815-chr12:9101960..9104335,2	MCF-7	breast:
2	chr12:9064351..9068260-chr12:9100706..9102986,3	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	chr12:9093611..9096195-chr12:9102368..9104030,2	K562	blood:
6	chr12:8849223..8851082-chr12:9101432..9104201,2	K562	blood:
7	chr12:9093100..9096905-chr12:9100746..9103868,4	K562	blood:
8	chr12:9081265..9083698-chr12:9100850..9103403,2	MCF-7	breast:
9	chr12:6643729..6644390-chr12:9101999..9102649,2	Hela-S3	cervix:
10	chr12:9100379..9103293-chr12:9215519..9218225,4	MCF-7	breast:
11	chr12:9096830..9100498-chr12:9102068..9104762,4	K562	blood:

Variant related genes	Relation type
KLRG1	TF binding region
M6PR	TF binding region
ENSG00000166532	Chromatin interaction
ENSG00000245105	Chromatin interaction
ENSG00000111752	Chromatin interaction
ENSG00000003056	Chromatin interaction
ENSG00000214851	Chromatin interaction
ENSG00000256004	Chromatin interaction
ENSG00000111640	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10129061	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10400516	0.81[ASN][1000 genomes]
rs10400563	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs10743568	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771238	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11048190	0.84[ASN][1000 genomes]
rs11048195	0.96[CHB][hapmap];0.84[ASN][1000 genomes]
rs11048264	0.81[ASN][1000 genomes]
rs11048337	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs11048338	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs11048344	0.83[ASN][1000 genomes]
rs11048345	0.83[ASN][1000 genomes]
rs1121401	0.85[ASN][1000 genomes]
rs11614202	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12423746	0.83[ASN][1000 genomes]
rs12423817	0.83[ASN][1000 genomes]
rs12424026	0.83[ASN][1000 genomes]
rs12812913	0.83[ASN][1000 genomes]
rs12821842	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs12823100	0.96[CHB][hapmap];0.83[ASN][1000 genomes]
rs12833375	0.83[ASN][1000 genomes]
rs1476911	0.91[CHB][hapmap]
rs1805248	1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1805724	0.96[CHB][hapmap];0.84[ASN][1000 genomes]
rs1805725	0.81[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1805727	0.81[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1805732	0.91[CHB][hapmap]
rs1805733	0.91[CHB][hapmap]
rs1805735	0.96[CHB][hapmap];0.81[ASN][1000 genomes]
rs1805754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805761	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs1805765	0.82[CHB][hapmap]
rs2041624	0.83[ASN][1000 genomes]
rs2041625	0.83[ASN][1000 genomes]
rs2284349	0.95[JPT][hapmap]
rs2377671	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2377672	0.82[ASN][1000 genomes]
rs2377673	0.83[ASN][1000 genomes]
rs2377674	0.83[ASN][1000 genomes]
rs2377676	0.85[ASN][1000 genomes]
rs34798934	0.83[ASN][1000 genomes]
rs4309200	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs4639983	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4883203	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6832	0.95[CHB][hapmap]
rs7132930	0.83[ASN][1000 genomes]
rs7300767	0.83[ASN][1000 genomes]
rs7301381	0.81[ASN][1000 genomes]
rs7957321	0.83[ASN][1000 genomes]
rs7961355	0.97[ASN][1000 genomes]
rs7974486	0.85[ASN][1000 genomes]
rs933462	0.96[CHB][hapmap];0.84[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
rs987917	M6PR	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9099400-9103600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr12:9099600-9103600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:9100200-9103400	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr12:9100200-9103800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:9100200-9103800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:9100400-9103600	Active TSS	HSMMtube	muscle
7	chr12:9100400-9103800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:9100400-9103800	Active TSS	Right Atrium	heart
9	chr12:9100400-9103800	Active TSS	K562	blood
10	chr12:9100400-9104000	Active TSS	GM12878-XiMat	blood
11	chr12:9100600-9103800	Active TSS	NHLF	lung
12	chr12:9100800-9103400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:9100800-9103600	Active TSS	H1 Cell Line	embryonic stem cell
14	chr12:9101000-9103400	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr12:9101000-9103400	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr12:9101000-9103600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:9101000-9103600	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr12:9101000-9103600	Active TSS	Fetal Intestine Small	intestine
19	chr12:9101000-9103600	Active TSS	Right Ventricle	heart
20	chr12:9101000-9103600	Active TSS	HSMM	muscle
21	chr12:9101000-9103800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:9101000-9103800	Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr12:9101000-9103800	Active TSS	Fetal Intestine Large	intestine
24	chr12:9101000-9104000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:9101000-9104400	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr12:9101200-9103000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:9101200-9103200	Active TSS	Placenta Amnion	Placenta Amnion
28	chr12:9101200-9103400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr12:9101200-9103400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:9101200-9103400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:9101200-9103400	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr12:9101200-9103400	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr12:9101200-9103400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr12:9101200-9103400	Active TSS	Primary monocytes fromperipheralblood	blood
35	chr12:9101200-9103400	Active TSS	Fetal Kidney	kidney
36	chr12:9101200-9103400	Active TSS	Fetal Muscle Trunk	muscle
37	chr12:9101200-9103400	Active TSS	Ovary	ovary
38	chr12:9101200-9103400	Active TSS	Hela-S3	cervix
39	chr12:9101200-9103600	Active TSS	H9 Cell Line	embryonic stem cell
40	chr12:9101200-9103600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:9101200-9103600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:9101200-9103600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:9101200-9103600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:9101200-9103600	Active TSS	Colonic Mucosa	Colon
45	chr12:9101200-9103600	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr12:9101200-9103600	Active TSS	NHDF-Ad	bronchial
47	chr12:9101200-9103800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:9101200-9103800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:9101200-9103800	Active TSS	Muscle Satellite Cultured Cells	--
50	chr12:9101200-9103800	Active TSS	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links