Variant report

Variant	rs59552665
Chromosome Location	chr5:27472002-27472003
allele	C/T
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	STAT3	chr5:27471790-27472853	Hela-S3	cervix:	n/a	n/a
2	MXI1	chr5:27471931-27472815	HepG2	liver:	n/a	n/a
3	POLR2A	chr5:27471986-27473289	HepG2	liver:	n/a	n/a
4	FOXA1	chr5:27471955-27472687	HepG2	liver:	n/a	n/a
5	TBP	chr5:27471898-27474340	Hela-S3	cervix:	n/a	n/a
6	ELK1	chr5:27471926-27472824	Hela-S3	cervix:	n/a	n/a
7	EBF1	chr5:27471957-27472434	GM12878	blood:	n/a	chr5:27472197-27472208
8	EBF1	chr5:27471930-27472591	GM12878	blood:	n/a	chr5:27472197-27472208
9	TCF12	chr5:27471947-27472777	A549	lung:	n/a	n/a
10	ARID3A	chr5:27471950-27472762	HepG2	liver:	n/a	n/a
11	FOXA2	chr5:27471684-27472617	HepG2	liver:	n/a	n/a
12	FOXA1	chr5:27471942-27472642	HepG2	liver:	n/a	n/a
13	POLR2A	chr5:27471861-27473974	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAX	chr5:27471993-27472777	A549	lung:	n/a	n/a
15	MAFK	chr5:27471707-27474892	Hela-S3	cervix:	n/a	chr5:27474076-27474091 chr5:27474700-27474715
16	GTF2F1	chr5:27471963-27472914	H1-hESC	embryonic stem cell:	n/a	n/a
17	FOXA1	chr5:27471990-27472652	HepG2	liver:	n/a	n/a
18	MYBL2	chr5:27471910-27472820	HepG2	liver:	n/a	n/a
19	FOXA2	chr5:27471954-27472635	A549	lung:	n/a	n/a
20	POLR2A	chr5:27471999-27473674	H1-hESC	embryonic stem cell:	n/a	n/a
21	SMC3	chr5:27471995-27474320	Hela-S3	cervix:	n/a	n/a
22	TEAD4	chr5:27472002-27473028	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
LINC01021	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs58284253	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59831890	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73069857	1.00[AMR][1000 genomes]
rs73069860	1.00[AMR][1000 genomes]
rs73069863	1.00[AMR][1000 genomes]
rs73071640	1.00[AMR][1000 genomes]
rs73071644	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881286	chr5:27135351-27770554	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv880298	chr5:27193573-27659111	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv880326	chr5:27193573-27743375	Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv880623	chr5:27279981-27559659	Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv881318	chr5:27323746-27559659	Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv881503	chr5:27344037-27510050	Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv881475	chr5:27376682-27510050	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv881003	chr5:27376682-27539490	Enhancers ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv880935	chr5:27376682-27559659	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv880535	chr5:27376682-27706007	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv881089	chr5:27387385-27478198	ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv881139	chr5:27388559-27539490	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	nsv880496	chr5:27388559-27559659	Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
14	nsv880940	chr5:27388559-27611431	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
15	nsv880999	chr5:27388559-27770554	Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
16	nsv880926	chr5:27401935-27539490	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
17	nsv881221	chr5:27401935-27660532	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
18	nsv881125	chr5:27406164-27622177	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
19	nsv880660	chr5:27418887-27510050	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
20	nsv880726	chr5:27424981-27539490	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
21	nsv880474	chr5:27424981-27559659	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
22	nsv880869	chr5:27424981-27684515	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
23	nsv597681	chr5:27426728-27526060	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
24	nsv1030914	chr5:27458599-27502029	Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
25	nsv881364	chr5:27464184-27611431	Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:27468400-27472200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr5:27471600-27472400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:27471800-27472200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr5:27471800-27472200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr5:27471800-27472200	Flanking Active TSS	A549	lung
6	chr5:27471800-27472200	Enhancers	HepG2	liver
7	chr5:27471800-27474600	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr5:27472000-27472200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:27472000-27472200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr5:27472000-27472200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr5:27472000-27472200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr5:27472000-27472400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:27472000-27472400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:27472000-27472600	Flanking Active TSS	Hela-S3	cervix
15	chr5:27472000-27474800	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr5:27472000-27474800	Active TSS	H1 Cell Line	embryonic stem cell
17	chr5:27472000-27475200	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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