Variant report

Variant	rs13353996
Chromosome Location	chr5:147237068-147237069
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	RAD21	chr5:147237054-147237562	HepG2	liver:	n/a	chr5:147237291-147237310 chr5:147237295-147237304
2	RAD21	chr5:147237036-147237550	H1-hESC	embryonic stem cell:	n/a	chr5:147237291-147237310 chr5:147237295-147237304
3	NRF1	chr5:147236518-147237358	H1-hESC	embryonic stem cell:	n/a	n/a
4	TEAD4	chr5:147237055-147237502	HepG2	liver:	n/a	chr5:147237343-147237352
5	POLR2A	chr5:147236079-147237070	H1-hESC	embryonic stem cell:	n/a	n/a
6	BRCA1	chr5:147236963-147237464	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr5:147230386-147238906	H1-hESC	embryonic stem cell:	n/a	n/a
8	RAD21	chr5:147237036-147237571	A549	lung:	n/a	chr5:147237291-147237310 chr5:147237295-147237304
9	RAD21	chr5:147237020-147237644	MCF-7	breast:	n/a	chr5:147237291-147237310 chr5:147237295-147237304
10	CEBPB	chr5:147237064-147237389	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr5:147230397-147244635	H1-hESC	embryonic stem cell:	n/a	n/a
12	RAD21	chr5:147236891-147237685	SK-N-SH	brain:	n/a	chr5:147237291-147237310 chr5:147237295-147237304 chr5:147236925-147236934
13	GTF2F1	chr5:147236867-147237696	H1-hESC	embryonic stem cell:	n/a	n/a
14	TAF7	chr5:147236300-147237494	H1-hESC	embryonic stem cell:	n/a	n/a
15	RAD21	chr5:147237045-147237559	MCF-7	breast:	n/a	chr5:147237291-147237310 chr5:147237295-147237304
16	RAD21	chr5:147236997-147237554	HCT-116	colon:	n/a	chr5:147237291-147237310 chr5:147237295-147237304
17	RAD21	chr5:147236998-147237573	HCT-116	colon:	n/a	chr5:147237291-147237310 chr5:147237295-147237304
18	ATF2	chr5:147237018-147237506	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr5:147237053-147237498	HCT-116	colon:	n/a	chr5:147237290-147237308 chr5:147237292-147237313 chr5:147237291-147237307
20	YY1	chr5:147237027-147237459	H1-hESC	embryonic stem cell:	n/a	chr5:147237220-147237228 chr5:147237219-147237231
21	CTCF	chr5:147237020-147237506	K562	blood:	n/a	chr5:147237290-147237308 chr5:147237292-147237313 chr5:147237291-147237307
22	CHD2	chr5:147230473-147237490	H1-hESC	embryonic stem cell:	n/a	n/a
23	ELF1	chr5:147236974-147237600	MCF-7	breast:	n/a	chr5:147237280-147237291 chr5:147237280-147237291
24	RAD21	chr5:147237035-147237556	A549	lung:	n/a	chr5:147237291-147237310 chr5:147237295-147237304
25	ATF2	chr5:147230878-147238649	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr5:147236999-147237605	MCF-7	breast:	n/a	chr5:147237290-147237308 chr5:147237292-147237313 chr5:147237291-147237307
27	CTCF	chr5:147236920-147237070	GM12874	blood:	n/a	n/a
28	SMC3	chr5:147236715-147237528	SK-N-SH	brain:	n/a	chr5:147237292-147237306
29	SMC3	chr5:147237067-147237453	HepG2	liver:	n/a	chr5:147237292-147237306
30	CHD1	chr5:147237056-147237476	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr5:147237059-147237483	MCF-7	breast:	n/a	chr5:147237290-147237308 chr5:147237292-147237313 chr5:147237291-147237307
32	CTCF	chr5:147236864-147237708	SK-N-SH	brain:	n/a	chr5:147237290-147237308 chr5:147237292-147237313 chr5:147237291-147237307
33	CTCF	chr5:147236740-147237765	A549	lung:	n/a	chr5:147237290-147237308 chr5:147237292-147237313 chr5:147237291-147237307
34	CTCF	chr5:147237020-147237170	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:147236987..147237740-chr5:147312978..147314003,3	MCF-7	breast:
2	chr5:147236815..147237790-chr5:147266317..147266844,2	K562	blood:
3	chr5:147236854..147237741-chr5:147314334..147315282,8	MCF-7	breast:
4	chr5:147007364..147008316-chr5:147236786..147237763,3	MCF-7	breast:
5	chr5:147236958..147237672-chr5:147259068..147259579,2	MCF-7	breast:
6	chr5:147236518..147237633-chr5:147314355..147315282,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249518	TF binding region
ENSG00000251320	Chromatin interaction
ENSG00000248362	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10039761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10040102	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10043586	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10078349	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12171507	0.82[LWK][hapmap]
rs13355958	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13360178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13360252	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28401755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28437385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28478293	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28479902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28570984	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28588162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28609427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28613022	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28684497	1.00[EUR][1000 genomes]
rs28707309	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59404183	1.00[EUR][1000 genomes]
rs60735175	1.00[EUR][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	nsv1021356	chr5:147103627-147310531	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1033907	chr5:147109014-147309076	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv537916	chr5:147109014-147309076	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3334831	chr5:147165950-147339765	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv933308	chr5:147173804-147269006	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147234200-147239600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:147234200-147262400	Weak transcription	Right Atrium	heart
3	chr5:147234400-147239800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:147234600-147237800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr5:147235000-147237400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:147235000-147239000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:147236800-147237200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr5:147236800-147239800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr5:147237000-147238400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr5:147237000-147243000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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