Variant report

Variant	rs597386
Chromosome Location	chr6:33668618-33668619
allele	A/C
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	RAD21	chr6:33667998-33668706	HCT-116	colon:	n/a	chr6:33668463-33668476 chr6:33668413-33668432 chr6:33668465-33668475
2	RAD21	chr6:33668143-33668685	MCF-7	breast:	n/a	chr6:33668463-33668476 chr6:33668413-33668432 chr6:33668465-33668475
3	POLR2A	chr6:33668204-33668665	HCT-116	colon:	n/a	n/a
4	FOXM1	chr6:33668068-33668657	GM12878	blood:	n/a	n/a
5	CTCF	chr6:33668224-33668619	K562	blood:	n/a	chr6:33668415-33668433 chr6:33668416-33668432 chr6:33668410-33668431 chr6:33668417-33668430
6	RAD21	chr6:33668232-33668645	ECC-1	luminal epithelium:	n/a	chr6:33668463-33668476 chr6:33668413-33668432 chr6:33668465-33668475
7	CTCF	chr6:33667959-33668855	HCT-116	colon:	n/a	chr6:33668415-33668433 chr6:33668416-33668432 chr6:33668410-33668431 chr6:33668417-33668430
8	RAD21	chr6:33667793-33668807	SK-N-SH	brain:	n/a	chr6:33668463-33668476 chr6:33668413-33668432 chr6:33668465-33668475
9	RAD21	chr6:33668157-33668659	MCF-7	breast:	n/a	chr6:33668463-33668476 chr6:33668413-33668432 chr6:33668465-33668475
10	ZC3H11A	chr6:33668231-33668631	K562	blood:	n/a	n/a
11	POLR2A	chr6:33668066-33668646	Hela-S3	cervix:	n/a	n/a
12	TCF12	chr6:33668204-33668828	A549	lung:	n/a	n/a
13	ZNF263	chr6:33668175-33668824	HEK293-T-REx	kidney:	n/a	n/a
14	CTCF	chr6:33668155-33668755	HCT-116	colon:	n/a	chr6:33668415-33668433 chr6:33668416-33668432 chr6:33668410-33668431 chr6:33668417-33668430
15	CTCF	chr6:33668164-33668618	A549	lung:	n/a	chr6:33668415-33668433 chr6:33668416-33668432 chr6:33668410-33668431 chr6:33668417-33668430
16	JUND	chr6:33668201-33668631	H1-hESC	embryonic stem cell:	n/a	chr6:33668308-33668317
17	CTCF	chr6:33668046-33668861	SK-N-SH	brain:	n/a	chr6:33668415-33668433 chr6:33668416-33668432 chr6:33668410-33668431 chr6:33668417-33668430
18	RAD21	chr6:33668162-33668621	SK-N-SH_RA	brain:	n/a	chr6:33668463-33668476 chr6:33668413-33668432 chr6:33668465-33668475
19	POLR2A	chr6:33668325-33668733	MCF10A-Er-Src	breast:	n/a	n/a
20	SMC3	chr6:33667735-33668829	SK-N-SH	brain:	n/a	chr6:33668465-33668475 chr6:33668417-33668431
21	POLR2A	chr6:33668022-33668647	PFSK-1	brain:	n/a	n/a
22	RAD21	chr6:33668174-33668640	IMR90	lung:	n/a	chr6:33668463-33668476 chr6:33668413-33668432 chr6:33668465-33668475
23	CTCF	chr6:33668073-33668721	K562	blood:	n/a	chr6:33668415-33668433 chr6:33668416-33668432 chr6:33668410-33668431 chr6:33668417-33668430
24	CTCF	chr6:33668206-33668627	K562	blood:	n/a	chr6:33668415-33668433 chr6:33668416-33668432 chr6:33668410-33668431 chr6:33668417-33668430
25	MAX	chr6:33668274-33668624	H1-hESC	embryonic stem cell:	n/a	n/a
26	RAD21	chr6:33668004-33668709	HCT-116	colon:	n/a	chr6:33668463-33668476 chr6:33668413-33668432 chr6:33668465-33668475
27	POLR2A	chr6:33668212-33668775	K562	blood:	n/a	n/a
28	POLR2A	chr6:33668347-33668813	MCF10A-Er-Src	breast:	n/a	n/a
29	RUNX3	chr6:33668167-33668631	GM12878	blood:	n/a	n/a
30	CTCF	chr6:33667885-33668973	A549	lung:	n/a	chr6:33668415-33668433 chr6:33668416-33668432 chr6:33668410-33668431 chr6:33668417-33668430
31	RAD21	chr6:33668155-33668655	HepG2	liver:	n/a	chr6:33668463-33668476 chr6:33668413-33668432 chr6:33668465-33668475
32	USF2	chr6:33668253-33668635	H1-hESC	embryonic stem cell:	n/a	n/a
33	RAD21	chr6:33668108-33668629	H1-hESC	embryonic stem cell:	n/a	chr6:33668463-33668476 chr6:33668413-33668432 chr6:33668465-33668475
34	SMC3	chr6:33668201-33668620	K562	blood:	n/a	chr6:33668465-33668475 chr6:33668417-33668431
35	CTCF	chr6:33668102-33668711	MCF-7	breast:	n/a	chr6:33668415-33668433 chr6:33668416-33668432 chr6:33668410-33668431 chr6:33668417-33668430
36	RAD21	chr6:33668137-33668697	A549	lung:	n/a	chr6:33668463-33668476 chr6:33668413-33668432 chr6:33668465-33668475
37	POLR2A	chr6:33668294-33668630	HCT-116	colon:	n/a	n/a
38	CTCF	chr6:33668222-33668639	MCF-7	breast:	n/a	chr6:33668415-33668433 chr6:33668416-33668432 chr6:33668410-33668431 chr6:33668417-33668430
39	CTCF	chr6:33668203-33668642	GM12878	blood:	n/a	chr6:33668415-33668433 chr6:33668416-33668432 chr6:33668410-33668431 chr6:33668417-33668430
40	POLR2A	chr6:33668198-33668658	K562	blood:	n/a	n/a
41	CTCF	chr6:33668217-33668630	IMR90	lung:	n/a	chr6:33668415-33668433 chr6:33668416-33668432 chr6:33668410-33668431 chr6:33668417-33668430
42	MTA3	chr6:33667963-33668686	GM12878	blood:	n/a	n/a
43	POLR2A	chr6:33668603-33668645	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr6:33668195-33668620	MCF-7	breast:	n/a	n/a
45	POLR2A	chr6:33668215-33668645	K562	blood:	n/a	n/a
46	POLR2A	chr6:33668025-33668964	SK-N-MC	brain:	n/a	n/a
47	RAD21	chr6:33668116-33668644	A549	lung:	n/a	chr6:33668463-33668476 chr6:33668413-33668432 chr6:33668465-33668475
48	POLR2A	chr6:33667851-33668907	PANC-1	pancreas:	n/a	n/a
49	BCLAF1	chr6:33668205-33668638	GM12878	blood:	n/a	n/a
50	CTCF	chr6:33668600-33668750	AG04449	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:33590320..33593181-chr6:33667665..33670096,2	MCF-7	breast:
2	chr6:33243707..33246364-chr6:33666916..33668671,2	MCF-7	breast:
3	chr6:33606352..33608133-chr6:33668168..33670127,2	K562	blood:
4	chr6:33661102..33664232-chr6:33667999..33669816,4	MCF-7	breast:
5	chr6:33554288..33554846-chr6:33668249..33668840,2	MCF-7	breast:
6	chr6:33553322..33554036-chr6:33667998..33668833,3	MCF-7	breast:
7	chr6:33557862..33560664-chr6:33667390..33670226,3	MCF-7	breast:
8	chr6:33557322..33558111-chr6:33667371..33668903,6	MCF-7	breast:
9	chr6:33553081..33555328-chr6:33667772..33669168,10	K562	blood:
10	chr6:33667241..33669923-chr6:33710850..33712681,2	K562	blood:
11	chr6:33557542..33558049-chr6:33667963..33668918,2	MCF-7	breast:
12	chr6:33556676..33558804-chr6:33667221..33669587,2	K562	blood:
13	chr6:33553773..33556336-chr6:33668184..33671160,4	MCF-7	breast:
14	chr6:33420892..33423040-chr6:33668080..33670301,2	MCF-7	breast:
15	chr6:33668029..33668860-chr6:34122128..34122772,2	K562	blood:
16	chr6:33553176..33554214-chr6:33667921..33668866,4	MCF-7	breast:
17	chr6:33667395..33669385-chr6:33670170..33673083,3	MCF-7	breast:
18	chr6:33557066..33558559-chr6:33667900..33669281,8	K562	blood:

Variant related genes	Relation type
UQCC2	TF binding region
ENSG00000213588	Chromatin interaction
ENSG00000269490	Chromatin interaction
ENSG00000235863	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10672	1.00[JPT][hapmap]
rs10947436	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs1536501	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs1998949	1.00[JPT][hapmap]
rs2182659	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs2395401	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs2395448	1.00[JPT][hapmap]
rs2967	1.00[JPT][hapmap]
rs4711350	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs498114	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs530614	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs549652	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs602399	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs608971	1.00[JPT][hapmap]
rs623813	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs652049	0.88[GIH][hapmap]
rs654682	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs658087	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs684119	0.92[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs688209	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs6913517	1.00[JPT][hapmap]
rs6915136	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs751727	1.00[JPT][hapmap]
rs764753	1.00[JPT][hapmap]
rs943463	1.00[JPT][hapmap]
rs943464	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs943472	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs9461905	1.00[JPT][hapmap]
rs9469542	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs597386	DEF6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33621400-33672600	Strong transcription	Dnd41	blood
2	chr6:33640000-33669200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:33650400-33669000	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:33660200-33669400	Strong transcription	HepG2	liver
5	chr6:33661400-33669200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr6:33661600-33668800	Genic enhancers	NHEK	skin
7	chr6:33661800-33675800	Weak transcription	Ovary	ovary
8	chr6:33662800-33669600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:33663000-33669000	Strong transcription	K562	blood
10	chr6:33663000-33678200	Weak transcription	Fetal Kidney	kidney
11	chr6:33663600-33669600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:33663800-33678600	Weak transcription	Small Intestine	intestine
13	chr6:33664600-33678000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:33664800-33669400	Strong transcription	Placenta	Placenta
15	chr6:33664800-33676200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:33665000-33668800	Genic enhancers	GM12878-XiMat	blood
17	chr6:33665200-33668800	Genic enhancers	Primary T cells from cord blood	blood
18	chr6:33665200-33668800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:33665200-33669000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:33665200-33678000	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:33665200-33678200	Weak transcription	Brain Substantia Nigra	brain
22	chr6:33665200-33678600	Weak transcription	Aorta	Aorta
23	chr6:33665400-33669400	Strong transcription	Osteobl	bone
24	chr6:33665400-33669600	Strong transcription	Stomach Smooth Muscle	stomach
25	chr6:33665400-33669800	Strong transcription	NHLF	lung
26	chr6:33665400-33670200	Weak transcription	Fetal Brain Male	brain
27	chr6:33665400-33672200	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr6:33665400-33677800	Weak transcription	Stomach Mucosa	stomach
29	chr6:33665600-33669600	Strong transcription	Hela-S3	cervix
30	chr6:33665600-33678200	Weak transcription	NH-A	brain
31	chr6:33665600-33678400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr6:33665800-33669400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:33665800-33676600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr6:33666000-33669000	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr6:33666000-33669600	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr6:33666000-33676200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:33666000-33676600	Weak transcription	Brain Angular Gyrus	brain
38	chr6:33666000-33677800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:33666000-33678200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr6:33666200-33669400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:33666200-33669400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr6:33666200-33677600	Weak transcription	Psoas Muscle	Psoas
43	chr6:33666400-33668800	Enhancers	Primary B cells from peripheral blood	blood
44	chr6:33666400-33669000	Genic enhancers	HMEC	breast
45	chr6:33666400-33677800	Weak transcription	Brain Anterior Caudate	brain
46	chr6:33666600-33668800	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr6:33666600-33669200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:33666600-33669200	Weak transcription	Fetal Brain Female	brain
49	chr6:33666600-33669400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr6:33666600-33669400	Strong transcription	Fetal Lung	lung

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