Variant report

Variant	rs540654
Chromosome Location	chr6:70930600-70930601
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	CTCF	chr6:70930476-70931335	A549	lung:	n/a	chr6:70930845-70930866 chr6:70930848-70930856 chr6:70930843-70930861
2	CTCF	chr6:70930491-70930612	GM12878	blood:	n/a	n/a
3	RAD21	chr6:70930584-70931039	H1-hESC	embryonic stem cell:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
4	CTCF	chr6:70930344-70931590	SK-N-SH	brain:	n/a	chr6:70930845-70930866 chr6:70930848-70930856 chr6:70930843-70930861
5	CTCF	chr6:70930484-70930625	Medullo	brain:	n/a	n/a
6	SMC3	chr6:70930565-70931507	SK-N-SH	brain:	n/a	chr6:70930845-70930859
7	CTCF	chr6:70930460-70930610	HPAF	blood vessel:	n/a	n/a
8	RAD21	chr6:70930276-70931857	SK-N-SH	brain:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
9	CUX1	chr6:70930552-70930908	K562	blood:	n/a	n/a
10	RAD21	chr6:70930584-70931169	A549	lung:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
11	CTCF	chr6:70930595-70931077	HCT-116	colon:	n/a	chr6:70930845-70930866 chr6:70930848-70930856 chr6:70930843-70930861

No.	Distal block	Cell Line	Cell type
1	chr6:70930597..70933117-chr6:70988758..70990429,2	K562	blood:
2	chr6:70930581..70931580-chr6:71078690..71079470,4	MCF-7	breast:
3	chr6:70930172..70932460-chr6:71107052..71108700,2	K562	blood:
4	chr6:70930395..70931237-chr6:71722269..71722995,2	K562	blood:

Variant related genes	Relation type
ENSG00000253809	TF binding region
ENSG00000112280	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1040655	0.85[CEU][hapmap]
rs1200562	0.93[GIH][hapmap]
rs1200564	1.00[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1200565	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1200566	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1200567	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1200574	1.00[ASW][hapmap];0.83[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes]
rs1517043	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[EUR][1000 genomes]
rs16868641	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs16868806	0.85[CEU][hapmap]
rs1711709	0.90[YRI][hapmap]
rs1753251	0.93[GIH][hapmap]
rs17690121	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs17712342	0.85[EUR][1000 genomes]
rs17747228	0.97[EUR][1000 genomes]
rs45486305	0.97[EUR][1000 genomes]
rs476026	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs476740	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs477680	1.00[ASW][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes]
rs487928	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs491690	0.89[YRI][hapmap]
rs513631	0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs531627	0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs558856	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs559027	0.94[AFR][1000 genomes]
rs577010	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs607716	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs628028	1.00[ASW][hapmap];0.85[MKK][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs637054	1.00[ASW][hapmap];0.83[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes]
rs652776	1.00[ASW][hapmap];0.83[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes]
rs661521	1.00[CEU][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6914511	0.85[CEU][hapmap];0.86[GIH][hapmap]
rs6923695	0.85[CEU][hapmap]
rs737331	0.85[EUR][1000 genomes]
rs73746881	0.97[EUR][1000 genomes]
rs802177	0.81[MKK][hapmap]
rs802181	1.00[ASW][hapmap];0.87[MKK][hapmap];0.90[YRI][hapmap]
rs802183	0.90[YRI][hapmap]
rs9446213	0.85[CEU][hapmap];0.86[GIH][hapmap]
rs9455013	0.85[CEU][hapmap];0.86[GIH][hapmap]

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	nsv1026151	chr6:70621616-70946967	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv933674	chr6:70663616-70973112	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv886142	chr6:70741209-71251421	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv830683	chr6:70743422-70941190	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:70918600-70930800	Weak transcription	Primary B cells from peripheral blood	blood
2	chr6:70930000-70932000	Enhancers	Duodenum Mucosa	Duodenum
3	chr6:70930200-70931600	Enhancers	Stomach Mucosa	stomach
4	chr6:70930200-70931800	Enhancers	Fetal Intestine Small	intestine
5	chr6:70930200-70932200	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr6:70930400-70932200	Enhancers	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links