Variant report

Variant	rs3130099
Chromosome Location	chr6:33282181-33282182
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	chr6:33281146-33283366	HUVEC	blood vessel:	n/a	n/a
2	EP300	chr6:33281578-33282506	GM12878	blood:	n/a	chr6:33281860-33281874
3	PML	chr6:33280132-33282847	GM12878	blood:	n/a	n/a
4	RCOR1	chr6:33281570-33283179	K562	blood:	n/a	n/a
5	POLR2A	chr6:33281097-33283399	PANC-1	pancreas:	n/a	n/a
6	MXI1	chr6:33281486-33283181	K562	blood:	n/a	n/a
7	EGR1	chr6:33282066-33282597	GM12878	blood:	n/a	chr6:33282071-33282084 chr6:33282075-33282085 chr6:33282076-33282086
8	REST	chr6:33281220-33282338	HL-60	blood:	n/a	n/a
9	TEAD4	chr6:33280036-33283539	K562	blood:	n/a	n/a
10	EP300	chr6:33281698-33282649	GM12878	blood:	n/a	chr6:33281860-33281874
11	NR2F2	chr6:33281524-33282992	K562	blood:	n/a	chr6:33282459-33282474
12	RELA	chr6:33280470-33282720	GM18505	blood:	n/a	chr6:33281902-33281911 chr6:33281902-33281911
13	NFATC1	chr6:33282080-33282721	GM12878	blood:	n/a	n/a
14	RAD21	chr6:33280948-33282567	IMR90	lung:	n/a	n/a
15	POLR2A	chr6:33280818-33283534	GM12892	blood:	n/a	n/a
16	RELA	chr6:33280347-33282735	GM10847	blood:	n/a	chr6:33281902-33281911 chr6:33281902-33281911
17	CHD1	chr6:33280438-33282580	GM12878	blood:	n/a	n/a
18	RUNX3	chr6:33280199-33282777	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:33280375-33283561	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr6:33280354-33283211	GM12892	blood:	n/a	n/a
21	POLR2A	chr6:33282079-33282635	HepG2	liver:	n/a	n/a
22	SIN3A	chr6:33280946-33283091	GM12878	blood:	n/a	n/a
23	POLR2A	chr6:33280288-33283297	MCF-7	breast:	n/a	n/a
24	BCL3	chr6:33281423-33282795	A549	lung:	n/a	chr6:33281860-33281869 chr6:33281866-33281875 chr6:33282075-33282084
25	STAT1	chr6:33281581-33282612	GM12878	blood:	n/a	chr6:33281864-33281875 chr6:33282071-33282083
26	RELA	chr6:33280373-33282911	GM19099	blood:	n/a	chr6:33281902-33281911 chr6:33281902-33281911
27	POLR2A	chr6:33280764-33283332	GM12892	blood:	n/a	n/a
28	POLR2A	chr6:33280121-33283446	K562	blood:	n/a	n/a
29	POLR2A	chr6:33281077-33282629	Hela-S3	cervix:	n/a	n/a
30	FOXM1	chr6:33281111-33282570	GM12878	blood:	n/a	n/a
31	TCF12	chr6:33281215-33283124	A549	lung:	n/a	chr6:33282034-33282044
32	SP1	chr6:33282071-33282683	A549	lung:	n/a	chr6:33282074-33282086 chr6:33282075-33282085 chr6:33282076-33282085 chr6:33282596-33282607 chr6:33282074-33282086 chr6:33282075-33282084 chr6:33282075-33282089
33	POLR2A	chr6:33280417-33283656	PBDE	blood:	n/a	n/a
34	PRDM1	chr6:33281603-33282309	Hela-S3	cervix:	n/a	chr6:33281863-33281872 chr6:33281856-33281870 chr6:33281861-33281876 chr6:33281857-33281870 chr6:33281862-33281876 chr6:33281863-33281876
35	ZBTB7A	chr6:33281780-33282192	K562	blood:	n/a	n/a
36	NR2F2	chr6:33282024-33282918	K562	blood:	n/a	chr6:33282459-33282474
37	EP300	chr6:33282134-33282754	A549	lung:	n/a	n/a
38	IRF1	chr6:33280345-33283267	K562	blood:	n/a	chr6:33281864-33281876 chr6:33281857-33281877 chr6:33281864-33281877 chr6:33281417-33281427 chr6:33281863-33281877 chr6:33281864-33281875 chr6:33280706-33280720 chr6:33281853-33281870 chr6:33281858-33281869 chr6:33281864-33281877 chr6:33281865-33281879 chr6:33281859-33281876 chr6:33281859-33281869 chr6:33281853-33281874 chr6:33281864-33281878 chr6:33281861-33281878 chr6:33281861-33281875 chr6:33282072-33282086 chr6:33281864-33281877 chr6:33281859-33281873 chr6:33281863-33281874 chr6:33281855-33281869 chr6:33281865-33281875
39	POLR2A	chr6:33280902-33283139	K562	blood:	n/a	n/a
40	TBP	chr6:33281306-33282506	HepG2	liver:	n/a	n/a
41	POLR2A	chr6:33281429-33282465	U87	brain:	n/a	n/a
42	EGR1	chr6:33281971-33282626	K562	blood:	n/a	chr6:33282071-33282084 chr6:33282075-33282085 chr6:33282076-33282086 chr6:33282015-33282025
43	HEY1	chr6:33281058-33282782	HepG2	liver:	n/a	n/a
44	POLR2A	chr6:33281386-33283170	HUVEC	blood vessel:	n/a	n/a
45	STAT5A	chr6:33281385-33282678	GM12878	blood:	n/a	chr6:33281864-33281875 chr6:33282071-33282083
46	TAF1	chr6:33281695-33282225	SK-N-SH	brain:	n/a	n/a
47	MXI1	chr6:33280324-33282669	HepG2	liver:	n/a	n/a
48	RCOR1	chr6:33281727-33282551	Hela-S3	cervix:	n/a	n/a
49	MAZ	chr6:33279967-33283766	IMR90	lung:	n/a	n/a
50	POLR2A	chr6:33280346-33282971	GM19193	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:33282156-33282206	Hela-S3	cervix:	n/a
2	chr6:33282175-33282225	ECC-1	luminal epithelium:	n/a
3	chr6:33282156-33282206	NB4	blood:	n/a
4	chr6:33282156-33282206	HRE	kidney:	n/a
5	chr6:33282175-33282225	ProgFib	skin:	n/a
6	chr6:33282175-33282225	HRCEpiC	kidney:	n/a
7	chr6:33282175-33282225	ovcar-3	ovarian:	n/a
8	chr6:33282175-33282225	HRPEpiC	eye:	n/a
9	chr6:33282156-33282206	U87	brain:	n/a
10	chr6:33282156-33282206	HepG2	liver:	n/a
11	chr6:33282175-33282225	H1-hESC	embryonic stem cell:	embryo
12	chr6:33282175-33282225	Caco-2	colon:	n/a
13	chr6:33282156-33282206	SK-N-SH_RA	brain:	n/a
14	chr6:33282175-33282225	AG10803	skin:	n/a
15	chr6:33282156-33282206	HL-60	blood:	n/a
16	chr6:33282156-33282206	HMEC	breast:	n/a
17	chr6:33282156-33282206	CMK	blood:	n/a
18	chr6:33282175-33282225	HIPEpiC	eye:	n/a
19	chr6:33282175-33282225	U87	brain:	n/a
20	chr6:33282175-33282225	GM06990	blood:	n/a
21	chr6:33282175-33282225	HCF	heart:	n/a
22	chr6:33282175-33282225	K562	blood:	n/a
23	chr6:33282175-33282225	HL-60	blood:	n/a
24	chr6:33282156-33282206	AG04449	skin:	fetal
25	chr6:33282175-33282225	GM19239	blood:	n/a
26	chr6:33282156-33282206	Caco-2	colon:	n/a
27	chr6:33282156-33282206	Hepatocyte	liver:	n/a
28	chr6:33282156-33282206	T-47D	breast:	n/a
29	chr6:33282175-33282225	NH-A	brain:	n/a
30	chr6:33282156-33282206	A549	lung:	n/a
31	chr6:33282156-33282206	H1-hESC	embryonic stem cell:	embryo
32	chr6:33282175-33282225	HUVEC	blood vessel:	n/a
33	chr6:33282175-33282225	HCM	heart:	n/a
34	chr6:33282156-33282206	LNCaP	prostate:	n/a
35	chr6:33282156-33282206	HUVEC	blood vessel:	n/a
36	chr6:33282175-33282225	AG09319	gingival:	n/a
37	chr6:33282175-33282225	SK-N-SH	brain:	n/a
38	chr6:33282156-33282206	HNPCEpiC	eye:	n/a
39	chr6:33282156-33282206	HCF	heart:	n/a
40	chr6:33282156-33282206	HCPEpiC	choroid plexus:	n/a
41	chr6:33282156-33282206	PFSK-1	brain:	n/a
42	chr6:33282175-33282225	NB4	blood:	n/a
43	chr6:33282175-33282225	GM12891	blood:	n/a
44	chr6:33282175-33282225	AoSMC	blood vessel:	n/a
45	chr6:33282175-33282225	AG04449	skin:	fetal
46	chr6:33282175-33282225	PrEC	prostate:	n/a
47	chr6:33282175-33282225	HEK293	kidney:	embryo
48	chr6:33282156-33282206	AG09309	skin:	n/a
49	chr6:33282156-33282206	MCF10A-Er-Src	breast:	n/a
50	chr6:33282156-33282206	Jurkat	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:33167013..33169892-chr6:33280381..33282720,3	MCF-7	breast:
2	chr6:33238090..33243099-chr6:33279379..33286881,12	MCF-7	breast:
3	chr6:33280452..33282497-chr6:33377188..33378997,2	MCF-7	breast:
4	chr6:32937349..32940364-chr6:33280292..33282198,3	MCF-7	breast:
5	chr6:33280766..33282554-chr6:33333161..33335162,2	K562	blood:
6	chr6:33280908..33284579-chr6:33359142..33361187,5	K562	blood:
7	chr6:33259755..33275794-chr6:33276314..33291745,68	MCF-7	breast:
8	chr6:33215997..33218425-chr6:33280174..33283199,3	K562	blood:
9	chr6:32936236..32938607-chr6:33279588..33282413,3	MCF-7	breast:
10	chr11:33757523..33758138-chr6:33281662..33282491,2	Hela-S3	cervix:
11	chr6:33279220..33282454-chr6:33357653..33360404,5	MCF-7	breast:
12	chr19:14529814..14530438-chr6:33281601..33282533,2	Hela-S3	cervix:
13	chr6:33280795..33292485-chr6:33374786..33387605,31	K562	blood:
14	chr16:56965612..56966446-chr6:33281998..33282624,2	Hela-S3	cervix:
15	chr6:33256218..33259091-chr6:33279064..33284854,6	MCF-7	breast:
16	chr17:7382482..7385239-chr6:33280198..33282715,2	MCF-7	breast:
17	chr6:33279097..33283546-chr6:33386045..33390564,5	MCF-7	breast:
18	chr6:33243260..33246626-chr6:33279357..33283682,8	MCF-7	breast:
19	chr6:33279489..33293095-chr6:33375317..33398824,56	K562	blood:
20	chr6:33281855..33283498-chr6:33357981..33360061,3	MCF-7	breast:
21	chr17:29233009..29233845-chr6:33281938..33282496,2	Hela-S3	cervix:
22	chr6:33280708..33283139-chr6:33358214..33362149,5	K562	blood:

Variant related genes	Relation type
TAPBP	TF binding region
TAPBP	CpG island
ENSG00000123136	Chromatin interaction
ENSG00000184060	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000172171	Chromatin interaction
ENSG00000259224	Chromatin interaction
ENSG00000204257	Chromatin interaction
ENSG00000051108	Chromatin interaction
ENSG00000197283	Chromatin interaction
ENSG00000237441	Chromatin interaction
ENSG00000227057	Chromatin interaction
ENSG00000112473	Chromatin interaction
ENSG00000223501	Chromatin interaction
ENSG00000112514	Chromatin interaction
ENSG00000085063	Chromatin interaction
ENSG00000235863	Chromatin interaction
ENSG00000204220	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000112511	Chromatin interaction
ENSG00000202441	Chromatin interaction
ENSG00000204231	Chromatin interaction
ENSG00000232940	Chromatin interaction
ENSG00000228285	Chromatin interaction
ENSG00000231500	Chromatin interaction
ENSG00000223837	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1014779	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1061783	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1800838	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2013891	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2071888	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2071889	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2395379	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2894334	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3106190	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3106195	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3130016	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3130018	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3130100	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3130101	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3130102	0.82[EUR][1000 genomes]
rs3130262	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3130263	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3130264	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3130265	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3130266	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3130267	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3130269	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3130270	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3130271	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3135405	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3135407	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3135408	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3135409	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs446735	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs456261	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs463260	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs464865	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs469064	0.80[EUR][1000 genomes]
rs9277968	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830634	chr6:33161217-33330745	Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3130099	TAPBP	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33279600-33282400	Active TSS	NHDF-Ad	bronchial
2	chr6:33279800-33282400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:33279800-33282600	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr6:33279800-33282600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:33279800-33282800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr6:33279800-33283000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:33279800-33283200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr6:33280000-33282200	Active TSS	Small Intestine	intestine
9	chr6:33280000-33282600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:33280000-33283000	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr6:33280000-33283200	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr6:33280200-33282200	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:33280200-33282200	Active TSS	A549	lung
14	chr6:33280200-33282400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:33280200-33282400	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr6:33280200-33282400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:33280200-33282400	Active TSS	Fetal Kidney	kidney
18	chr6:33280200-33282400	Active TSS	Lung	lung
19	chr6:33280200-33282400	Active TSS	Sigmoid Colon	Sigmoid Colon
20	chr6:33280200-33282400	Active TSS	Stomach Mucosa	stomach
21	chr6:33280200-33282400	Active TSS	GM12878-XiMat	blood
22	chr6:33280200-33282400	Active TSS	NHLF	lung
23	chr6:33280200-33282600	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr6:33280200-33282600	Active TSS	Ovary	ovary
25	chr6:33280200-33283200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr6:33280400-33282200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:33280400-33282200	Active TSS	Thymus	Thymus
28	chr6:33280400-33282400	Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr6:33280400-33282400	Active TSS	Colon Smooth Muscle	Colon
30	chr6:33280400-33282400	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr6:33280400-33282400	Flanking Active TSS	Fetal Brain Male	brain
32	chr6:33280400-33282400	Active TSS	Fetal Intestine Large	intestine
33	chr6:33280400-33282400	Active TSS	Spleen	Spleen
34	chr6:33280400-33282400	Bivalent/Poised TSS	HepG2	liver
35	chr6:33280400-33282400	Active TSS	HMEC	breast
36	chr6:33280400-33282400	Active TSS	NHEK	skin
37	chr6:33280400-33282600	Active TSS	H1 Cell Line	embryonic stem cell
38	chr6:33280400-33282600	Active TSS	Aorta	Aorta
39	chr6:33280400-33283000	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr6:33280600-33282200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:33280600-33282200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:33280600-33282200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:33280600-33282200	Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr6:33280600-33282200	Active TSS	Primary B cells from cord blood	blood
45	chr6:33280600-33282200	Active TSS	Primary B cells from peripheral blood	blood
46	chr6:33280600-33282200	Active TSS	Primary T cells from cord blood	blood
47	chr6:33280600-33282200	Active TSS	Primary T cells fromperipheralblood	blood
48	chr6:33280600-33282200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr6:33280600-33282200	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr6:33280600-33282200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links