Variant report

Variant	rs9261402
Chromosome Location	chr6:30069137-30069138
allele	C/T
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	HDAC2	chr6:30068189-30069146	HepG2	liver:	n/a	n/a
2	MAX	chr6:30068086-30071338	HCT-116	colon:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
3	MBD4	chr6:30068218-30069187	HepG2	liver:	n/a	n/a
4	TEAD4	chr6:30068212-30069469	HepG2	liver:	n/a	n/a
5	POLR2A	chr6:30068376-30071409	HepG2	liver:	n/a	n/a
6	POLR2A	chr6:30069116-30069420	HepG2	liver:	n/a	n/a
7	MAX	chr6:30067884-30071564	HepG2	liver:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
8	POLR2A	chr6:30068290-30071350	HepG2	liver:	n/a	n/a
9	MYBL2	chr6:30068021-30071300	HepG2	liver:	n/a	n/a
10	MYC	chr6:30068574-30070009	MCF10A-Er-Src	breast:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
11	MAX	chr6:30068117-30069148	HCT-116	colon:	n/a	chr6:30068716-30068725
12	E2F6	chr6:30067832-30070137	H1-hESC	embryonic stem cell:	n/a	chr6:30069962-30069972 chr6:30068213-30068220 chr6:30069998-30070008 chr6:30068208-30068218 chr6:30068209-30068220 chr6:30068213-30068220 chr6:30069967-30069976 chr6:30068213-30068220 chr6:30068406-30068413 chr6:30068209-30068217 chr6:30068208-30068219 chr6:30068209-30068217
13	MAX	chr6:30068260-30070212	MCF-7	breast:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
14	POLR2A	chr6:30069003-30070273	HepG2	liver:	n/a	n/a
15	CTCF	chr6:30069080-30069230	BJ	skin:	n/a	n/a
16	CREB1	chr6:30068194-30071311	HepG2	liver:	n/a	n/a
17	E2F6	chr6:30069134-30070065	H1-hESC	embryonic stem cell:	n/a	chr6:30069962-30069972 chr6:30069998-30070008 chr6:30069967-30069976
18	MAX	chr6:30069109-30069352	HepG2	liver:	n/a	chr6:30069316-30069323 chr6:30069315-30069324
19	EGR1	chr6:30068208-30069167	HCT-116	colon:	n/a	chr6:30068696-30068706 chr6:30068731-30068744
20	POLR2A	chr6:30068758-30069431	HepG2	liver:	n/a	n/a
21	MAX	chr6:30069083-30070134	K562	blood:	n/a	chr6:30069316-30069323 chr6:30069315-30069324
22	MAX	chr6:30067993-30070449	HepG2	liver:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
23	HEY1	chr6:30068212-30071230	HepG2	liver:	n/a	chr6:30070002-30070017 chr6:30069966-30069981
24	MBD4	chr6:30068252-30070257	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30031338..30034907-chr6:30068673..30070684,4	MCF-7	breast:
2	chr6:30039673..30045870-chr6:30065915..30071954,9	MCF-7	breast:
3	chr6:30059482..30063646-chr6:30064744..30071169,8	MCF-7	breast:
4	chr6:30037077..30039641-chr6:30068261..30070312,3	MCF-7	breast:
5	chr6:30068376..30069897-chr6:30103951..30105962,2	MCF-7	breast:
6	chr6:30068684..30075353-chr6:30179679..30184952,7	MCF-7	breast:
7	chr6:30004933..30007814-chr6:30068168..30069816,2	MCF-7	breast:
8	chr6:30029240..30031636-chr6:30067690..30069434,2	K562	blood:
9	chr6:30031856..30036259-chr6:30064937..30071315,10	MCF-7	breast:
10	chr6:30027986..30030809-chr6:30067690..30071011,4	K562	blood:
11	chr6:30059663..30061808-chr6:30067229..30070058,2	K562	blood:
12	chr6:30028086..30030535-chr6:30068315..30071049,3	MCF-7	breast:
13	chr6:30067195..30070112-chr6:30098151..30100617,2	MCF-7	breast:
14	chr6:30039276..30042217-chr6:30067253..30069841,2	K562	blood:
15	chr6:30024946..30027912-chr6:30068442..30070614,2	MCF-7	breast:
16	chr6:30068547..30070487-chr6:30073986..30076858,2	K562	blood:
17	chr6:30063791..30066840-chr6:30067476..30070156,3	MCF-7	breast:
18	chr6:30067592..30070049-chr6:30312859..30314391,2	K562	blood:
19	chr6:30054838..30057804-chr6:30069131..30071158,2	MCF-7	breast:
20	chr6:30046314..30047956-chr6:30068316..30070912,2	MCF-7	breast:

Variant related genes	Relation type
TRIM31-AS1	TF binding region
ENSG00000241370	Chromatin interaction
ENSG00000204616	Chromatin interaction
ENSG00000204619	Chromatin interaction
ENSG00000066379	Chromatin interaction
ENSG00000252901	Chromatin interaction
ENSG00000204614	Chromatin interaction
ENSG00000204623	Chromatin interaction
ENSG00000234127	Chromatin interaction
ENSG00000204618	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1061536	0.86[EUR][1000 genomes]
rs3094145	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3121593	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3121595	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3121596	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3130397	0.91[ASN][1000 genomes]
rs3132128	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3132130	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3132675	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3132676	0.91[ASN][1000 genomes]
rs3132683	0.95[EUR][1000 genomes]
rs3134881	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3893259	0.87[EUR][1000 genomes]
rs4472395	0.87[EUR][1000 genomes]
rs4959036	0.87[EUR][1000 genomes]
rs5025708	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6539	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6928431	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7763159	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9260676	0.87[EUR][1000 genomes]
rs9260685	0.87[EUR][1000 genomes]
rs9260702	0.87[EUR][1000 genomes]
rs9260706	0.87[EUR][1000 genomes]
rs9260761	0.87[EUR][1000 genomes]
rs9260786	0.87[EUR][1000 genomes]
rs9260808	0.89[EUR][1000 genomes]
rs9260857	0.92[EUR][1000 genomes]
rs9260973	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9260997	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9261061	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9261136	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9261142	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9261143	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9261211	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9261212	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9261269	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9261434	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261494	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv884051	chr6:30059451-30071279	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv884050	chr6:30059451-30071330	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv884053	chr6:30059592-30070538	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
5	nsv884054	chr6:30061361-30069525	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30064800-30069600	Bivalent Enhancer	Fetal Thymus	thymus
2	chr6:30068000-30069200	Bivalent Enhancer	Placenta	Placenta
3	chr6:30068000-30069800	Enhancers	Lung	lung
4	chr6:30068000-30072600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr6:30068200-30069200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:30068200-30069400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
7	chr6:30068200-30069800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:30068200-30069800	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr6:30068200-30070200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:30068200-30071800	Flanking Active TSS	NHEK	skin
11	chr6:30068400-30069200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr6:30068400-30069200	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr6:30068400-30069200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
14	chr6:30068400-30069200	Bivalent/Poised TSS	NH-A	brain
15	chr6:30068400-30069400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:30068400-30069400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr6:30068400-30069400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
18	chr6:30068400-30069400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
19	chr6:30068400-30069400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
20	chr6:30068400-30069400	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood
21	chr6:30068400-30069400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
22	chr6:30068400-30069400	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
23	chr6:30068400-30069400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
24	chr6:30068400-30069400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
25	chr6:30068400-30069400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
26	chr6:30068400-30069400	Bivalent Enhancer	Fetal Heart	heart
27	chr6:30068400-30069400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
28	chr6:30068400-30069600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:30068400-30069600	Flanking Active TSS	Colonic Mucosa	Colon
30	chr6:30068400-30069600	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
31	chr6:30068400-30069600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
32	chr6:30068400-30069600	Bivalent/Poised TSS	NHLF	lung
33	chr6:30068400-30069800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
34	chr6:30068400-30069800	Flanking Active TSS	Pancreas	Pancrea
35	chr6:30068400-30069800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr6:30068400-30069800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
37	chr6:30068400-30069800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
38	chr6:30068400-30070000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:30068400-30070000	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
40	chr6:30068400-30070200	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:30068400-30070200	Flanking Active TSS	HMEC	breast
42	chr6:30068400-30070400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr6:30068400-30071200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:30068600-30069200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
45	chr6:30068600-30069400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
46	chr6:30068600-30069400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
47	chr6:30068600-30069400	Flanking Active TSS	Esophagus	oesophagus
48	chr6:30068600-30069400	Bivalent Enhancer	Fetal Brain Male	brain
49	chr6:30068600-30069600	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:30068600-30069800	Flanking Bivalent TSS/Enh	Thymus	Thymus

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