Variant report

Variant	rs28780106
Chromosome Location	chr6:30451515-30451516
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:68)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:68 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:30451500-30451650	NHLF	lung:	n/a	n/a
2	CTCF	chr6:30451435-30451843	A549	lung:	n/a	n/a
3	RAD21	chr6:30451459-30451960	IMR90	lung:	n/a	n/a
4	CTCF	chr6:30451454-30451800	SK-N-SH_RA	brain:	n/a	n/a
5	CTCF	chr6:30451478-30451786	HepG2	liver:	n/a	n/a
6	CTCF	chr6:30451502-30451716	LNCaP	prostate:	n/a	n/a
7	CTCF	chr6:30451509-30451783	H1-hESC	embryonic stem cell:	n/a	n/a
8	RAD21	chr6:30451380-30451823	MCF-7	breast:	n/a	n/a
9	CTCF	chr6:30451495-30451783	ECC-1	luminal epithelium:	n/a	n/a
10	ZNF143	chr6:30451506-30451802	GM12878	blood:	n/a	n/a
11	CTCF	chr6:30451380-30451530	GM12868	blood:	n/a	n/a
12	RAD21	chr6:30451452-30451865	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr6:30451434-30451873	K562	blood:	n/a	n/a
14	CTCF	chr6:30451458-30451817	MCF-7	breast:	n/a	n/a
15	CTCF	chr6:30451509-30451809	K562	blood:	n/a	n/a
16	ARID3A	chr6:30451477-30451801	K562	blood:	n/a	n/a
17	RAD21	chr6:30451418-30451868	MCF-7	breast:	n/a	n/a
18	RAD21	chr6:30451488-30451789	A549	lung:	n/a	n/a
19	CTCF	chr6:30451418-30451866	HCT-116	colon:	n/a	n/a
20	CTCF	chr6:30451438-30451825	Spleen_OC	spleen:	n/a	n/a
21	CTCF	chr6:30451184-30452003	HCT-116	colon:	n/a	n/a
22	RAD21	chr6:30451469-30451834	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr6:30450976-30452031	SK-N-SH	brain:	n/a	n/a
24	FOXM1	chr6:30451426-30451834	GM12878	blood:	n/a	n/a
25	RAD21	chr6:30451452-30451839	Hela-S3	cervix:	n/a	n/a
26	CTCF	chr6:30451391-30451837	K562	blood:	n/a	n/a
27	RAD21	chr6:30451410-30451852	GM12878	blood:	n/a	n/a
28	CTCF	chr6:30451402-30451907	A549	lung:	n/a	n/a
29	SMC3	chr6:30451480-30451824	HepG2	liver:	n/a	n/a
30	RAD21	chr6:30451225-30452070	SK-N-SH	brain:	n/a	n/a
31	SMC3	chr6:30451465-30451866	GM12878	blood:	n/a	n/a
32	RAD21	chr6:30451482-30451825	A549	lung:	n/a	n/a
33	CTCF	chr6:30451460-30451610	A549	lung:	n/a	n/a
34	SMC3	chr6:30451484-30451791	K562	blood:	n/a	n/a
35	RAD21	chr6:30451395-30451867	A549	lung:	n/a	n/a
36	RAD21	chr6:30451441-30451829	HepG2	liver:	n/a	n/a
37	CTCF	chr6:30451500-30451650	HFF-Myc	foreskin:	n/a	n/a
38	MAFF	chr6:30451512-30451752	K562	blood:	n/a	n/a
39	RAD21	chr6:30451354-30451953	HepG2	liver:	n/a	n/a
40	CTCF	chr6:30451402-30451991	HepG2	liver:	n/a	n/a
41	CTCF	chr6:30451498-30451783	ECC-1	luminal epithelium:	n/a	n/a
42	RAD21	chr6:30451431-30451884	ECC-1	luminal epithelium:	n/a	n/a
43	ZNF143	chr6:30451510-30451792	K562	blood:	n/a	n/a
44	CTCF	chr6:30451480-30451630	RPTEC	kidney:	n/a	n/a
45	CTCF	chr6:30451381-30451778	MCF-7	breast:	n/a	n/a
46	RCOR1	chr6:30451515-30451797	K562	blood:	n/a	n/a
47	SMC3	chr6:30451472-30451832	Hela-S3	cervix:	n/a	n/a
48	MYC	chr6:30451493-30451754	K562	blood:	n/a	n/a
49	RAD21	chr6:30451446-30451857	GM12878	blood:	n/a	n/a
50	RAD21	chr6:30451482-30451800	HepG2	liver:	n/a	n/a

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30449909..30451600-chr6:30563747..30566713,2	K562	blood:
2	chr6:30451178..30452036-chr6:30512187..30513102,3	MCF-7	breast:
3	chr6:30451112..30451938-chr6:30464212..30465175,3	K562	blood:
4	chr6:30449686..30451639-chr6:30582069..30585092,3	MCF-7	breast:
5	chr6:30451337..30455149-chr6:30456477..30458768,3	MCF-7	breast:
6	chr6:30450075..30454964-chr6:30456336..30460057,8	MCF-7	breast:
7	chr6:30451219..30453103-chr6:30692483..30694829,2	K562	blood:
8	chr6:30451245..30452270-chr6:30511951..30513069,6	MCF-7	breast:
9	chr6:30451366..30455453-chr6:30455599..30459533,6	K562	blood:
10	chr6:30449909..30452819-chr6:30563358..30566713,3	K562	blood:
11	chr6:30446384..30451689-chr6:30578094..30585004,12	MCF-7	breast:
12	chr6:30448715..30451618-chr6:30508372..30511107,3	MCF-7	breast:
13	chr6:30450855..30453185-chr6:30509734..30512303,2	K562	blood:
14	chr6:30450826..30454342-chr6:30455231..30458641,4	K562	blood:
15	chr6:30451165..30451756-chr6:30640464..30641301,2	K562	blood:
16	chr6:30448170..30453321-chr6:30582822..30586539,6	K562	blood:
17	chr6:30450929..30459545-chr6:30516289..30528141,20	K562	blood:
18	chr6:30451171..30452124-chr6:30499936..30500898,4	K562	blood:
19	chr6:30450665..30453098-chr6:30612269..30613984,2	MCF-7	breast:
20	chr6:30451203..30451876-chr6:30500417..30501033,3	MCF-7	breast:
21	chr6:30451134..30452078-chr6:30564843..30565849,4	K562	blood:
22	chr6:30451229..30451980-chr6:30564853..30565655,2	MCF-7	breast:
23	chr6:30447949..30451648-chr6:30569801..30572499,4	MCF-7	breast:
24	chr6:30435930..30438658-chr6:30450135..30452374,2	K562	blood:
25	chr6:30451190..30452121-chr6:30512183..30513107,8	K562	blood:

No data

Variant related genes	Relation type
RANP1	TF binding region
ENSG00000204568	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000204592	Chromatin interaction
ENSG00000204560	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000224936	Chromatin interaction
ENSG00000222894	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17195054	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17475879	0.86[ASN][1000 genomes]
rs28780101	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28780102	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28780104	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28780105	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28780108	0.86[EUR][1000 genomes]
rs35554791	0.93[ASN][1000 genomes]
rs3734843	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
4	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
5	nsv884070	chr6:30430875-30472772	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
6	nsv884076	chr6:30434566-30483919	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
7	nsv884077	chr6:30434900-30512163	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30450000-30453800	Weak transcription	Spleen	Spleen
2	chr6:30450200-30454400	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr6:30450200-30455600	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr6:30450400-30452600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr6:30450400-30455400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr6:30451400-30451600	Enhancers	Primary B cells from peripheral blood	blood
7	chr6:30451400-30451600	Enhancers	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links