Variant report

Variant	rs2996413
Chromosome Location	chr13:87377473-87377474
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr13:87377407-87377759	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr13:87377345-87377677	SK-N-SH_RA	brain:	n/a	n/a
3	RAD21	chr13:87377328-87377751	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr13:87377440-87377590	HMF	breast:	n/a	n/a
5	CTCF	chr13:87377462-87377658	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr13:87377460-87377610	RPTEC	kidney:	n/a	n/a
7	CTCF	chr13:87377452-87377579	HepG2	liver:	n/a	n/a
8	RAD21	chr13:87377323-87377699	SK-N-SH_RA	brain:	n/a	n/a
9	CTCF	chr13:87377460-87377610	HA-sp	spinal cord:	n/a	n/a
10	CTCF	chr13:87377459-87377669	Medullo	brain:	n/a	n/a
11	RAD21	chr13:87377413-87377694	HepG2	liver:	n/a	n/a
12	CTCF	chr13:87377345-87377645	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr13:87377409-87377730	GM12878	blood:	n/a	n/a
14	CTCF	chr13:87377380-87377530	RPTEC	kidney:	n/a	n/a
15	RAD21	chr13:87377182-87377844	SK-N-SH	brain:	n/a	n/a
16	CTCF	chr13:87377440-87377590	HAc	cerebellar:	n/a	n/a
17	CTCF	chr13:87377459-87377648	SK-N-SH_RA	brain:	n/a	n/a
18	CTCF	chr13:87377460-87377610	HCT-116	colon:	n/a	n/a
19	RAD21	chr13:87377286-87377747	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr13:87377460-87377610	SK-N-SH_RA	brain:	n/a	n/a
21	CTCF	chr13:87377358-87377761	SK-N-SH	brain:	n/a	n/a
22	CTCF	chr13:87377440-87377590	HEK293	kidney:	n/a	n/a
23	SMC3	chr13:87377298-87377879	SK-N-SH	brain:	n/a	n/a
24	CTCF	chr13:87377459-87377625	SK-N-SH_RA	brain:	n/a	n/a
25	RAD21	chr13:87377323-87377689	HepG2	liver:	n/a	n/a

No data

Variant related genes	Relation type
TXNL1P1	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12869804	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2996397	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2996407	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2996411	0.83[CHB][hapmap]
rs3015518	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs3015520	0.82[CHB][hapmap]
rs3015537	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4514536	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9301725	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9556075	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047136	chr13:86979109-87555131	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv900763	chr13:87073397-87658986	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv900773	chr13:87159109-87463100	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv562621	chr13:87192747-87927450	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1038179	chr13:87199973-87391741	Active TSS Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv2753866	chr13:87260025-87495281	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1052214	chr13:87283152-87428272	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv562624	chr13:87304859-87496155	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv900775	chr13:87311967-87658986	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1045701	chr13:87335640-87436713	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv3396494	chr13:87358000-87398086	Enhancers Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv3372753	chr13:87366000-87398086	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	esv3323042	chr13:87374000-87398086	Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	esv3398570	chr13:87376035-87392952	Inactive region	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:0 , 50 per page) page:

No data

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links