Variant report

Variant	rs9257445
Chromosome Location	chr6:28949206-28949207
allele	C/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	MTA3	chr6:28948934-28950362	GM12878	blood:	n/a	n/a
2	MXI1	chr6:28948484-28950141	K562	blood:	n/a	n/a
3	POLR2A	chr6:28948576-28949242	Hela-S3	cervix:	n/a	n/a
4	PML	chr6:28947951-28951078	K562	blood:	n/a	n/a
5	IRF4	chr6:28949199-28950267	GM12878	blood:	n/a	n/a
6	STAT5A	chr6:28947432-28950928	K562	blood:	n/a	chr6:28948572-28948584 chr6:28948629-28948643 chr6:28948631-28948640 chr6:28950129-28950140 chr6:28949208-28949216 chr6:28948632-28948641 chr6:28948571-28948583
7	ZNF384	chr6:28948415-28950109	K562	blood:	n/a	n/a
8	SP1	chr6:28948314-28950218	HepG2	liver:	n/a	chr6:28948570-28948584 chr6:28949811-28949821 chr6:28948569-28948581 chr6:28948571-28948580 chr6:28948569-28948581 chr6:28949811-28949821 chr6:28948576-28948585 chr6:28949824-28949845 chr6:28948575-28948589
9	ZMIZ1	chr6:28948100-28949539	K562	blood:	n/a	n/a
10	BHLHE40	chr6:28948970-28950167	GM12878	blood:	n/a	n/a
11	TEAD4	chr6:28949180-28950261	ECC-1	luminal epithelium:	n/a	n/a
12	CTCF	chr6:28949200-28949350	SAEC	small airway:	n/a	n/a
13	POLR2A	chr6:28947749-28949398	HepG2	liver:	n/a	n/a
14	ARID3A	chr6:28948436-28950785	HepG2	liver:	n/a	chr6:28949587-28949603
15	POLR2A	chr6:28948168-28949264	K562	blood:	n/a	n/a
16	SREBP2	chr6:28947887-28951126	GM12878	blood:	n/a	n/a
17	CEBPB	chr6:28948156-28951133	K562	blood:	n/a	chr6:28950989-28951001
18	CTCF	chr6:28949080-28949230	SAEC	small airway:	n/a	n/a
19	KAP1	chr6:28948148-28951514	HEK293	kidney:	n/a	n/a
20	TBP	chr6:28948794-28950182	K562	blood:	n/a	n/a
21	HEY1	chr6:28948095-28949678	HepG2	liver:	n/a	n/a
22	USF1	chr6:28948651-28949209	K562	blood:	n/a	n/a
23	POLR2A	chr6:28948368-28949374	HepG2	liver:	n/a	n/a
24	MAZ	chr6:28948393-28950877	K562	blood:	n/a	chr6:28949524-28949533
25	RAD21	chr6:28948877-28949243	HepG2	liver:	n/a	n/a
26	GTF2F1	chr6:28948484-28949490	K562	blood:	n/a	n/a
27	MYC	chr6:28948388-28951379	K562	blood:	n/a	chr6:28949524-28949533
28	TEAD4	chr6:28948295-28950960	HepG2	liver:	n/a	n/a
29	MYBL2	chr6:28948301-28950935	HepG2	liver:	n/a	n/a
30	STAT1	chr6:28948339-28950132	Hela-S3	cervix:	n/a	chr6:28948572-28948584 chr6:28948629-28948643 chr6:28948631-28948640 chr6:28949208-28949216 chr6:28948632-28948641 chr6:28948571-28948583
31	MXI1	chr6:28948789-28949476	Hela-S3	cervix:	n/a	n/a
32	TCF7L2	chr6:28949197-28949468	PANC-1	pancreas:	n/a	n/a
33	POLR2A	chr6:28948404-28949302	HepG2	liver:	n/a	n/a
34	STAT1	chr6:28949113-28950123	GM12878	blood:	n/a	chr6:28949208-28949216
35	TBP	chr6:28948936-28950272	HepG2	liver:	n/a	n/a
36	ZNF143	chr6:28948851-28950080	Hela-S3	cervix:	n/a	chr6:28949762-28949781
37	HEY1	chr6:28947621-28949623	HepG2	liver:	n/a	n/a
38	GATA1	chr6:28948082-28949292	PBDE	blood:	n/a	n/a
39	CTCF	chr6:28948712-28950086	A549	lung:	n/a	chr6:28949813-28949829
40	ZNF143	chr6:28948373-28949442	K562	blood:	n/a	n/a
41	POLR2A	chr6:28948127-28949262	K562	blood:	n/a	n/a
42	JUND	chr6:28948431-28949231	HepG2	liver:	n/a	n/a
43	MBD4	chr6:28948390-28950707	HepG2	liver:	n/a	n/a
44	CTCF	chr6:28949080-28949230	GM12872	blood:	n/a	n/a
45	TBP	chr6:28948824-28950652	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr6:28948388-28949272	K562	blood:	n/a	n/a
47	TEAD4	chr6:28949169-28950647	SK-N-SH	brain:	n/a	n/a
48	CEBPB	chr6:28948470-28950674	Hela-S3	cervix:	n/a	n/a
49	SMC3	chr6:28948889-28949298	HepG2	liver:	n/a	n/a
50	MYC	chr6:28948388-28950650	K562	blood:	n/a	chr6:28949524-28949533

No.	Distal block	Cell Line	Cell type
1	chr6:28948706..28953416-chr6:28959003..28967079,12	K562	blood:
2	chr6:28946686..28952098-chr6:28981757..28987491,9	K562	blood:
3	chr6:28829291..28833354-chr6:28946684..28949723,4	K562	blood:
4	chr6:28804861..28808227-chr6:28947720..28951878,5	K562	blood:
5	chr6:28907253..28915101-chr6:28945522..28952393,17	K562	blood:
6	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:
7	chr6:28723907..28726622-chr6:28947645..28950512,2	K562	blood:
8	chr6:28687246..28689887-chr6:28948960..28952398,3	K562	blood:
9	chr6:28861427..28869364-chr6:28946251..28954176,23	K562	blood:
10	chr6:28863945..28866493-chr6:28948972..28951087,2	MCF-7	breast:
11	chr6:28916972..28925607-chr6:28947207..28951909,14	K562	blood:
12	chr6:28829291..28833978-chr6:28947381..28950490,6	K562	blood:
13	chr6:28928142..28929743-chr6:28947588..28949383,2	K562	blood:
14	chr6:28948083..28951244-chr6:28977635..28980493,3	K562	blood:
15	chr6:28861427..28866893-chr6:28947878..28954176,14	K562	blood:
16	chr6:28889573..28894329-chr6:28949030..28952998,8	K562	blood:
17	chr6:28889725..28893274-chr6:28947221..28952049,9	MCF-7	breast:
18	chr6:28948241..28954799-chr6:28970209..28976187,12	MCF-7	breast:
19	chr6:27791369..27793553-chr6:28948965..28950721,2	K562	blood:
20	chr6:28888560..28894615-chr6:28945306..28952099,20	K562	blood:
21	chr6:28907996..28910654-chr6:28948439..28951310,2	MCF-7	breast:
22	chr6:28678329..28679999-chr6:28949047..28951282,2	K562	blood:

Variant related genes	Relation type
HCG15	TF binding region
ENSG00000204713	Chromatin interaction
ENSG00000197238	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000225173	Chromatin interaction
ENSG00000204709	Chromatin interaction
ENSG00000225595	Chromatin interaction
ENSG00000197935	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs4565335	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6909302	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6918712	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6919044	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6919687	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6923005	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6924824	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6925178	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6930903	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6933976	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7741520	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7743837	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7744689	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7744795	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7749435	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7764481	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9348822	0.85[AFR][1000 genomes]
rs9380105	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9461498	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9461499	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9468473	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9501291	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1023540	chr6:28922691-29326018	Active TSS Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
4	nsv538169	chr6:28922691-29326018	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv869541	chr6:28922692-29326017	Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv916439	chr6:28922697-29326087	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv462668	chr6:28922719-29342775	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	nsv601213	chr6:28922719-29342775	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv1015796	chr6:28923980-29342825	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv462669	chr6:28936556-29337500	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
11	nsv601214	chr6:28936556-29337500	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
12	nsv601215	chr6:28946920-29348297	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28948200-28950800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr6:28948200-28950800	Active TSS	Brain Anterior Caudate	brain
3	chr6:28948200-28951000	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr6:28948200-28951000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:28948400-28949400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr6:28948400-28950600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:28948400-28950600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:28948400-28950600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:28948400-28950600	Active TSS	Brain Cingulate Gyrus	brain
10	chr6:28948400-28950600	Active TSS	Fetal Heart	heart
11	chr6:28948400-28950600	Active TSS	Fetal Kidney	kidney
12	chr6:28948400-28950600	Active TSS	Rectal Smooth Muscle	rectum
13	chr6:28948400-28950600	Active TSS	HSMM	muscle
14	chr6:28948400-28950800	Active TSS	H9 Cell Line	embryonic stem cell
15	chr6:28948400-28950800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:28948400-28950800	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr6:28948400-28950800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:28948400-28950800	Active TSS	Brain Germinal Matrix	brain
19	chr6:28948400-28950800	Active TSS	Brain Substantia Nigra	brain
20	chr6:28948400-28950800	Active TSS	Right Ventricle	heart
21	chr6:28948400-28950800	Active TSS	A549	lung
22	chr6:28948400-28951000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:28948400-28951000	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr6:28948400-28951000	Active TSS	Brain Hippocampus Middle	brain
25	chr6:28948400-28951000	Active TSS	Fetal Brain Female	brain
26	chr6:28948400-28951000	Active TSS	Stomach Smooth Muscle	stomach
27	chr6:28948400-28951000	Active TSS	HSMMtube	muscle
28	chr6:28948400-28951800	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr6:28948600-28949400	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr6:28948600-28949400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr6:28948600-28949600	Active TSS	HepG2	liver
32	chr6:28948600-28950000	Active TSS	Gastric	stomach
33	chr6:28948600-28950600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:28948600-28950600	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr6:28948600-28950600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr6:28948600-28950600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr6:28948600-28950600	Active TSS	Colon Smooth Muscle	Colon
38	chr6:28948600-28950600	Active TSS	Fetal Intestine Large	intestine
39	chr6:28948600-28950600	Active TSS	Stomach Mucosa	stomach
40	chr6:28948600-28950800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr6:28948600-28950800	Active TSS	H1 Cell Line	embryonic stem cell
42	chr6:28948600-28950800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:28948600-28950800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:28948600-28951000	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr6:28948600-28951000	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr6:28948600-28951000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr6:28948600-28951000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:28948600-28951000	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr6:28948600-28951000	Active TSS	Ovary	ovary
50	chr6:28948600-28951600	Active TSS	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links