Variant report

Variant	rs2593490
Chromosome Location	chr13:69880976-69880977
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	CTCF	chr13:69880880-69881030	RPTEC	kidney:	n/a	n/a
2	FOXA1	chr13:69880966-69881122	T-47D	breast:	n/a	n/a
3	RAD21	chr13:69880942-69881269	Hela-S3	cervix:	n/a	n/a
4	FOXA1	chr13:69880863-69881145	T-47D	breast:	n/a	n/a
5	RAD21	chr13:69880975-69881232	SK-N-SH_RA	brain:	n/a	n/a
6	RAD21	chr13:69880847-69881203	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr13:69880878-69881252	H1-neurons	neurons:	n/a	n/a
8	RAD21	chr13:69880918-69881286	SK-N-SH	brain:	n/a	n/a
9	RAD21	chr13:69880942-69881272	H1-hESC	embryonic stem cell:	n/a	n/a
10	RAD21	chr13:69880970-69881274	ECC-1	luminal epithelium:	n/a	n/a
11	RAD21	chr13:69880960-69881251	MCF-7	breast:	n/a	n/a
12	RAD21	chr13:69880962-69881234	MCF-7	breast:	n/a	n/a
13	CTCF	chr13:69880963-69881255	GM12878	blood:	n/a	n/a
14	E2F4	chr13:69880852-69881019	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:69880056..69883403-chr13:69894393..69896223,3	K562	blood:

Variant related genes	Relation type
LINC00401	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1249772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1249773	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1249774	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1249775	0.92[ASN][1000 genomes]
rs1446384	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs1446385	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1572427	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1572428	0.83[CHB][hapmap]
rs17605284	0.92[ASN][1000 genomes]
rs1838808	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1853310	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1853311	0.94[ASN][1000 genomes]
rs1855899	0.96[ASN][1000 genomes]
rs1867797	0.90[ASN][1000 genomes]
rs2065839	0.92[ASN][1000 genomes]
rs2065840	0.99[ASN][1000 genomes]
rs2121288	0.92[ASN][1000 genomes]
rs2325208	0.94[ASN][1000 genomes]
rs2782484	0.89[EUR][1000 genomes]
rs34456127	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58043375	0.82[ASN][1000 genomes]
rs7325342	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326647	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7327635	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7336505	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7989827	0.94[ASN][1000 genomes]
rs921059	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9317793	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9317797	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9317800	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9529557	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9529558	0.99[ASN][1000 genomes]
rs9541879	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9541880	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9564552	0.82[ASN][1000 genomes]
rs9564561	0.92[ASN][1000 genomes]
rs9564564	0.90[ASN][1000 genomes]
rs9572128	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9572144	0.92[ASN][1000 genomes]
rs9572150	0.91[ASN][1000 genomes]
rs9572151	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9599445	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs967685	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs989143	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv1049303	chr13:69238676-69923558	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1038918	chr13:69251052-69919763	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv541829	chr13:69251052-69919763	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv900479	chr13:69824819-69984297	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv974213	chr13:69877439-69889811	Inactive region	TF binding region Chromatin interactive region lncRNA	2 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