Variant report

Variant	rs9257395
Chromosome Location	chr6:28911260-28911261
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	HEY1	chr6:28911072-28911475	K562	blood:	n/a	n/a
2	SP1	chr6:28911226-28911683	GM12878	blood:	n/a	chr6:28911570-28911584 chr6:28911527-28911534
3	MTA3	chr6:28911178-28912616	GM12878	blood:	n/a	n/a
4	YY1	chr6:28911255-28911738	HepG2	liver:	n/a	n/a
5	GTF2F1	chr6:28911165-28911677	K562	blood:	n/a	n/a
6	GTF3C2	chr6:28910983-28911776	K562	blood:	n/a	n/a
7	IRF1	chr6:28911183-28911697	K562	blood:	n/a	chr6:28911500-28911514 chr6:28911501-28911515 chr6:28911495-28911516 chr6:28911499-28911510 chr6:28911500-28911513 chr6:28911500-28911513 chr6:28911497-28911511 chr6:28911500-28911511 chr6:28911501-28911511
8	ATF3	chr6:28911012-28911867	A549	lung:	n/a	n/a
9	POLR2A	chr6:28911027-28911627	K562	blood:	n/a	n/a
10	MBD4	chr6:28911084-28911967	HepG2	liver:	n/a	n/a
11	SIN3A	chr6:28911180-28912489	H1-hESC	embryonic stem cell:	n/a	n/a
12	TEAD4	chr6:28911233-28911795	H1-hESC	embryonic stem cell:	n/a	n/a
13	TAF1	chr6:28911131-28911379	K562	blood:	n/a	n/a
14	TEAD4	chr6:28911251-28911756	A549	lung:	n/a	n/a
15	MYBL2	chr6:28911035-28911828	HepG2	liver:	n/a	n/a
16	NR2F2	chr6:28910796-28912776	K562	blood:	n/a	n/a
17	POLR2A	chr6:28911170-28911638	PANC-1	pancreas:	n/a	n/a
18	TEAD4	chr6:28910944-28912774	HepG2	liver:	n/a	n/a
19	GABPA	chr6:28911230-28911614	Hela-S3	cervix:	n/a	n/a
20	YY1	chr6:28911208-28911585	K562	blood:	n/a	n/a
21	HMGN3	chr6:28911186-28911597	K562	blood:	n/a	n/a
22	BATF	chr6:28911255-28911572	GM12878	blood:	n/a	chr6:28911535-28911544
23	EP300	chr6:28910905-28911835	K562	blood:	n/a	chr6:28911283-28911297
24	HSF1	chr6:28911202-28911661	HepG2	liver:	n/a	n/a
25	ATF3	chr6:28910961-28912792	A549	lung:	n/a	n/a
26	UBTF	chr6:28911196-28911683	K562	blood:	n/a	n/a
27	SP1	chr6:28911142-28911695	A549	lung:	n/a	chr6:28911570-28911584 chr6:28911527-28911534
28	TEAD4	chr6:28910938-28912912	K562	blood:	n/a	n/a
29	ZNF143	chr6:28911185-28911678	K562	blood:	n/a	n/a
30	ARID3A	chr6:28911238-28911775	HepG2	liver:	n/a	n/a
31	MYC	chr6:28911041-28912055	K562	blood:	n/a	n/a
32	USF1	chr6:28911187-28911677	A549	lung:	n/a	n/a
33	KAP1	chr6:28910979-28912613	HEK293	kidney:	n/a	chr6:28911291-28911299 chr6:28912510-28912518
34	IRF4	chr6:28911156-28911746	GM12878	blood:	n/a	chr6:28911499-28911513 chr6:28911495-28911516
35	EP300	chr6:28911221-28911705	GM12878	blood:	n/a	chr6:28911283-28911297
36	TEAD4	chr6:28911185-28911797	ECC-1	luminal epithelium:	n/a	n/a
37	MBD4	chr6:28911072-28911863	HepG2	liver:	n/a	n/a
38	POU2F2	chr6:28911174-28911721	GM12878	blood:	n/a	n/a
39	TEAD4	chr6:28911156-28911808	ECC-1	luminal epithelium:	n/a	n/a
40	PML	chr6:28911173-28912688	GM12878	blood:	n/a	chr6:28911291-28911299 chr6:28912510-28912518
41	CREB1	chr6:28911084-28912613	HepG2	liver:	n/a	n/a
42	POU2F2	chr6:28911184-28911660	GM12891	blood:	n/a	n/a
43	CBX3	chr6:28910835-28912713	K562	blood:	n/a	n/a
44	BCL11A	chr6:28911207-28911647	GM12878	blood:	n/a	chr6:28911502-28911511
45	SPI1	chr6:28911181-28911487	K562	blood:	n/a	n/a
46	PAX5	chr6:28911121-28911688	GM12878	blood:	n/a	chr6:28911502-28911511
47	CBX3	chr6:28911175-28911791	K562	blood:	n/a	n/a
48	TBP	chr6:28911189-28912548	K562	blood:	n/a	n/a
49	ZMIZ1	chr6:28911213-28911954	K562	blood:	n/a	n/a
50	TBL1XR1	chr6:28911131-28911696	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:28888957..28894217-chr6:28902105..28913114,27	MCF-7	breast:
2	chr6:28859278..28869415-chr6:28906395..28912460,18	K562	blood:
3	chr6:28583985..28585633-chr6:28910730..28913227,2	K562	blood:
4	chr6:28909868..28911383-chr6:28971101..28973508,2	K562	blood:
5	chr6:28886838..28893375-chr6:28904762..28912890,19	K562	blood:
6	chr6:28803772..28808857-chr6:28906937..28913057,11	K562	blood:
7	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:
8	chr6:27775703..27777987-chr6:28908653..28911644,2	K562	blood:

Variant related genes	Relation type
C6orf100	TF binding region
ENSG00000204713	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000227214	Chromatin interaction
ENSG00000197935	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000263426	Chromatin interaction
ENSG00000225173	Chromatin interaction
ENSG00000232040	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1061625	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs172326	0.80[ASN][1000 genomes]
rs1794588	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs209127	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs209140	0.82[ASN][1000 genomes]
rs209147	0.81[ASN][1000 genomes]
rs2097424	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2894066	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3130843	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3131067	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3131098	0.81[AMR][1000 genomes]
rs3132377	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3132380	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs393309	0.82[AMR][1000 genomes]
rs413972	0.80[ASN][1000 genomes]
rs429369	0.81[ASN][1000 genomes]
rs6906953	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6912843	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6926892	0.85[ASN][1000 genomes]
rs7740125	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7750338	0.81[ASN][1000 genomes]
rs7769221	0.81[ASN][1000 genomes]
rs876737	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9257328	0.81[ASN][1000 genomes]
rs9257399	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9257412	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9257416	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9257424	0.80[ASN][1000 genomes]
rs9257425	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[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	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
3	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28906600-28912600	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:28907400-28912400	Active TSS	H1 Cell Line	embryonic stem cell
3	chr6:28907400-28912400	Active TSS	H9 Cell Line	embryonic stem cell
4	chr6:28907400-28912400	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr6:28907400-28912400	Active TSS	A549	lung
6	chr6:28907400-28912800	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:28907400-28913400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:28907800-28912400	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr6:28907800-28912400	Active TSS	Rectal Smooth Muscle	rectum
10	chr6:28909400-28911400	Weak transcription	Gastric	stomach
11	chr6:28909400-28911400	Weak transcription	Lung	lung
12	chr6:28909600-28911400	Weak transcription	Aorta	Aorta
13	chr6:28909600-28911400	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr6:28909800-28911600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:28910000-28911400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:28910000-28911400	Weak transcription	Ovary	ovary
17	chr6:28910000-28911400	Weak transcription	Stomach Mucosa	stomach
18	chr6:28910000-28911400	Weak transcription	NH-A	brain
19	chr6:28910200-28911400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:28910200-28911400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:28910200-28911400	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr6:28910200-28911400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr6:28910200-28911400	Weak transcription	HSMMtube	muscle
24	chr6:28910200-28912400	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr6:28910200-28912400	Active TSS	Brain Angular Gyrus	brain
26	chr6:28910400-28911400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr6:28910400-28911400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr6:28910600-28912400	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr6:28910800-28911400	Enhancers	Fetal Muscle Leg	muscle
30	chr6:28910800-28911400	Enhancers	Placenta	Placenta
31	chr6:28910800-28911600	Active TSS	HepG2	liver
32	chr6:28911000-28911400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr6:28911000-28911400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr6:28911000-28911400	Active TSS	Adipose Nuclei	Adipose
35	chr6:28911000-28911400	Enhancers	HMEC	breast
36	chr6:28911000-28911400	Enhancers	HUVEC	blood vessel
37	chr6:28911000-28911600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:28911000-28911600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr6:28911000-28911600	Enhancers	Esophagus	oesophagus
40	chr6:28911000-28911600	Active TSS	Fetal Lung	lung
41	chr6:28911000-28911800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr6:28911000-28912000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr6:28911000-28912000	Flanking Active TSS	Brain Cingulate Gyrus	brain
44	chr6:28911000-28912000	Flanking Active TSS	Brain Hippocampus Middle	brain
45	chr6:28911000-28912200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:28911000-28912200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr6:28911000-28912200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr6:28911000-28912400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr6:28911000-28912400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr6:28911000-28912400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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