Variant report

Variant	rs12903381
Chromosome Location	chr15:50648940-50648941
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:42)
CpG islands
(count:0)
Chromatin interactive
region (count:27)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:42 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr15:50648766-50649032	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:50648747-50649607	HepG2	liver:	n/a	n/a
3	POLR2A	chr15:50645890-50649461	GM18505	blood:	n/a	n/a
4	POLR2A	chr15:50643941-50650733	GM12891	blood:	n/a	n/a
5	POLR2A	chr15:50648646-50650254	GM12892	blood:	n/a	n/a
6	POLR2A	chr15:50645476-50650223	GM12878	blood:	n/a	n/a
7	POLR2A	chr15:50646827-50649588	HepG2	liver:	n/a	n/a
8	POLR2A	chr15:50645950-50649548	K562	blood:	n/a	n/a
9	MTA3	chr15:50645838-50649091	GM12878	blood:	n/a	n/a
10	POLR2A	chr15:50643964-50649543	GM12878	blood:	n/a	n/a
11	POLR2A	chr15:50645530-50650223	K562	blood:	n/a	n/a
12	POLR2A	chr15:50648531-50650361	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr15:50648641-50649498	GM12891	blood:	n/a	n/a
14	POLR2A	chr15:50645808-50650538	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr15:50645464-50650252	K562	blood:	n/a	n/a
16	POLR2A	chr15:50645959-50649428	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr15:50646787-50650247	K562	blood:	n/a	n/a
18	POLR2A	chr15:50648927-50650213	GM12892	blood:	n/a	n/a
19	POLR2A	chr15:50648648-50650323	SK-N-MC	brain:	n/a	n/a
20	POLR2A	chr15:50648916-50649409	GM12891	blood:	n/a	n/a
21	CHD1	chr15:50645052-50649822	IMR90	lung:	n/a	chr15:50647640-50647650 chr15:50646931-50646941
22	POLR2A	chr15:50648702-50650294	MCF-7	breast:	n/a	n/a
23	POLR2A	chr15:50648563-50649654	PANC-1	pancreas:	n/a	n/a
24	HEY1	chr15:50648829-50649304	K562	blood:	n/a	n/a
25	POLR2A	chr15:50645847-50649076	HepG2	liver:	n/a	n/a
26	POLR2A	chr15:50648710-50650269	GM12878	blood:	n/a	n/a
27	MXI1	chr15:50644670-50649694	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr15:50645929-50649031	ProgFib	skin:	n/a	n/a
29	POLR2A	chr15:50643912-50651678	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr15:50648713-50650325	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr15:50643981-50656245	MCF10A-Er-Src	breast:	n/a	n/a
32	TBL1XR1	chr15:50648742-50649220	K562	blood:	n/a	n/a
33	POLR2A	chr15:50644647-50648996	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr15:50648495-50649703	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr15:50646088-50651672	Hela-S3	cervix:	n/a	n/a
36	HCFC1	chr15:50645295-50649087	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr15:50648818-50650254	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr15:50646019-50649543	PANC-1	pancreas:	n/a	n/a
39	POLR2A	chr15:50644838-50649712	IMR90	lung:	n/a	n/a
40	POLR2A	chr15:50648627-50649455	GM12892	blood:	n/a	n/a
41	POLR2A	chr15:50645312-50650230	GM12878	blood:	n/a	n/a
42	MYC	chr15:50646908-50649003	MCF10A-Er-Src	breast:	n/a	chr15:50647687-50647697

No data

(count:27 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:50645594..50649830-chr15:50754186..50757976,9	MCF-7	breast:
2	chr15:50646435..50649191-chr15:52859384..52862079,2	MCF-7	breast:
3	chr15:50643045..50650563-chr15:50756489..50761004,9	MCF-7	breast:
4	chr15:50647013..50649194-chr15:51198882..51202798,3	K562	blood:
5	chr15:50471646..50476620-chr15:50646050..50650091,9	MCF-7	breast:
6	chr15:50647163..50649970-chr15:50707470..50713022,5	MCF-7	breast:
7	chr15:50644389..50649393-chr15:50787180..50791359,7	MCF-7	breast:
8	chr15:50646264..50649073-chr17:62500886..62503658,2	MCF-7	breast:
9	chr15:50645553..50650972-chr15:51199033..51203961,11	MCF-7	breast:
10	chr15:50647220..50649637-chr15:50708002..50709799,2	K562	blood:
11	chr15:50513432..50516110-chr15:50646563..50649335,2	MCF-7	breast:
12	chr15:50552898..50556236-chr15:50646166..50649137,4	K562	blood:
13	chr11:66486776..66489307-chr15:50646648..50649417,2	MCF-7	breast:
14	chr15:50644809..50652796-chr15:50713240..50720627,20	K562	blood:
15	chr15:50646198..50649019-chr15:50789771..50791870,3	MCF-7	breast:
16	chr15:50645588..50649349-chr15:50728196..50732461,4	MCF-7	breast:
17	chr15:50646468..50650762-chr15:50786083..50789645,4	K562	blood:
18	chr15:50646359..50649336-chr15:50872616..50874692,3	MCF-7	breast:
19	chr15:50644978..50654282-chr15:50714279..50723145,48	MCF-7	breast:
20	chr15:50646763..50649574-chr8:128746981..128748587,2	MCF-7	breast:
21	chr15:50644601..50650486-chr15:50714318..50720349,10	K562	blood:
22	chr15:50644770..50653815-chr15:50713287..50720249,51	MCF-7	breast:
23	chr15:50646196..50649637-chr15:50705519..50710625,4	K562	blood:
24	chr15:50647970..50649936-chr15:50757455..50759138,2	K562	blood:
25	chr15:50648117..50650493-chr15:50779482..50782033,2	K562	blood:
26	chr15:50647443..50649396-chr15:50783549..50786868,3	MCF-7	breast:
27	chr11:20407767..20409374-chr15:50647141..50649461,2	MCF-7	breast:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USP8-2	chr15:50648297-50650501	ENSG00000244879
2	lnc-USP8-2	chr15:50648668-50649115	ENSG00000244879.2
3	lnc-USP8-2	chr15:50646371-50650503	NONHSAT042406
4	lnc-USP8-2	chr15:50648297-50650501	NONHSAT042411
5	lnc-USP8-2	chr15:50648297-50650527	ENSG00000244879.2

No data

Variant related genes	Relation type
MIR4712	TF binding region
GABPB1	TF binding region
ENSG00000092439	Chromatin interaction
ENSG00000200605	Chromatin interaction
ENSG00000259298	Chromatin interaction
ENSG00000185238	Chromatin interaction
ENSG00000173898	Chromatin interaction
ENSG00000242737	Chromatin interaction
ENSG00000136997	Chromatin interaction
ENSG00000140284	Chromatin interaction
ENSG00000258890	Chromatin interaction
ENSG00000138592	Chromatin interaction
ENSG00000104043	Chromatin interaction
ENSG00000140287	Chromatin interaction
ENSG00000108654	Chromatin interaction
ENSG00000259618	Chromatin interaction
ENSG00000252376	Chromatin interaction
ENSG00000128989	Chromatin interaction
ENSG00000259465	Chromatin interaction
ENSG00000081014	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 29 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1056681	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070770	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070772	1.00[ASN][1000 genomes]
rs11855995	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857071	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440601	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909202	0.86[GIH][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917303	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17509458	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17598020	1.00[ASN][1000 genomes]
rs2013885	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013888	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2033114	1.00[ASN][1000 genomes]
rs2414049	0.89[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28450641	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45508400	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504781	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022563	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022564	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022565	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022567	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022569	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022570	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493426	0.86[GIH][hapmap];0.95[MEX][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677143	0.85[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71424053	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72738935	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72738949	0.82[EUR][1000 genomes]
rs8034849	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920021	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
4	nsv948579	chr15:50645530-51045564	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

mRNA abundance (count:29)

SNP	Gene	Cis/trans	Tissue	Source
rs12903381	GABPB1-AS1	cis	Muscle Skeletal	GTEx
rs12903381	CTD-3110H11.1	cis	Nerve Tibial	GTEx
rs12903381	GABPB1-AS1	cis	Heart Left Ventricle	GTEx
rs12903381	GABPB1-AS1	cis	Esophagus Muscularis	GTEx
rs12903381	GABPB1-AS1	cis	Esophagus Mucosa	GTEx
rs12903381	CTD-3110H11.1	cis	Esophagus Muscularis	GTEx
rs12903381	CTD-3110H11.1	cis	Adipose Subcutaneous	GTEx
rs12903381	LOC100129387	cis	cerebellar cortex	BrainEAC
rs12903381	CTD-3110H11.1	cis	Muscle Skeletal	GTEx
rs12903381	LOC100129387	cis	occipital cortex	BrainEAC
rs12903381	GABPB1-AS1	cis	Stomach	GTEx
rs12903381	GABPB1-AS1	cis	Whole Blood	GTEx
rs12903381	CTD-3110H11.1	cis	Stomach	GTEx
rs12903381	GABPB1-AS1	cis	Nerve Tibial	GTEx
rs12903381	CTD-3110H11.1	cis	Skin Sun Exposed Lower leg	GTEx
rs12903381	LOC100129387	cis	temporal cortex	BrainEAC
rs12903381	GABPB2	Cis_1M	lymphoblastoid	RTeQTL
rs12903381	CTD-3110H11.1	cis	Thyroid	GTEx
rs12903381	GABPB1-AS1	cis	Artery Aorta	GTEx
rs12903381	GABPB1-AS1	cis	lung	GTEx
rs12903381	LOC100129387	cis	brain	BrainEAC
rs12903381	CTD-3110H11.1	cis	lung	GTEx
rs12903381	C15orf43	cis	parietal	SCAN
rs12903381	CTD-3110H11.1	cis	Esophagus Mucosa	GTEx
rs12903381	GABPB1-AS1	cis	Artery Tibial	GTEx
rs12903381	GABPB1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs12903381	GABPB1-AS1	cis	Adipose Subcutaneous	GTEx
rs12903381	GABPB1-AS1	cis	Thyroid	GTEx
rs12903381	CTD-3110H11.1	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50644400-50649000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr15:50644400-50649200	Active TSS	Fetal Brain Female	brain
3	chr15:50644400-50649400	Active TSS	NHLF	lung
4	chr15:50644600-50649200	Active TSS	H1 Cell Line	embryonic stem cell
5	chr15:50644600-50649200	Active TSS	GM12878-XiMat	blood
6	chr15:50644600-50649800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:50644800-50649200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr15:50644800-50649200	Active TSS	Right Ventricle	heart
9	chr15:50645000-50649000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:50645000-50649000	Active TSS	Primary T cells fromperipheralblood	blood
11	chr15:50645000-50649000	Active TSS	Fetal Muscle Leg	muscle
12	chr15:50645000-50649000	Active TSS	NHDF-Ad	bronchial
13	chr15:50645000-50649200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:50645000-50649200	Active TSS	Fetal Thymus	thymus
15	chr15:50645000-50649600	Active TSS	Psoas Muscle	Psoas
16	chr15:50645200-50649000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:50645400-50649400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr15:50645600-50649000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:50645600-50649600	Active TSS	H9 Cell Line	embryonic stem cell
20	chr15:50647000-50649400	Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr15:50647200-50649000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:50647400-50649200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:50647600-50649000	Active TSS	Brain Germinal Matrix	brain
24	chr15:50647800-50649000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:50647800-50649000	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr15:50647800-50649000	Active TSS	Right Atrium	heart
27	chr15:50647800-50649200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr15:50647800-50649400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr15:50647800-50649600	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr15:50647800-50649600	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr15:50647800-50649600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr15:50647800-50649600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:50647800-50649800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:50648000-50649000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr15:50648000-50649000	Flanking Active TSS	Liver	Liver
36	chr15:50648000-50649000	Flanking Active TSS	Brain Hippocampus Middle	brain
37	chr15:50648000-50649000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
38	chr15:50648000-50649000	Weak transcription	Gastric	stomach
39	chr15:50648000-50667600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr15:50648200-50649000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr15:50648200-50649000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr15:50648200-50649000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr15:50648200-50649000	Flanking Active TSS	Colon Smooth Muscle	Colon
44	chr15:50648200-50649200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr15:50648200-50649200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr15:50648200-50649400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:50648200-50649400	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr15:50648200-50649600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr15:50648200-50650000	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr15:50648200-50653800	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links