Variant report

Variant	rs59288996
Chromosome Location	chr18:30156582-30156583
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	RAD21	chr18:30156210-30156695	H1-hESC	embryonic stem cell:	n/a	chr18:30156439-30156452 chr18:30156436-30156455
2	GATA2	chr18:30156379-30156835	SH-SY5Y	brain:	n/a	chr18:30156383-30156392
3	CTCF	chr18:30156338-30156600	H1-hESC	embryonic stem cell:	n/a	chr18:30156435-30156453 chr18:30156438-30156451 chr18:30156438-30156447
4	RAD21	chr18:30156006-30157005	SK-N-SH	brain:	n/a	chr18:30156439-30156452 chr18:30156436-30156455
5	CTCF	chr18:30156257-30156656	MCF-7	breast:	n/a	chr18:30156435-30156453 chr18:30156438-30156451 chr18:30156438-30156447
6	RAD21	chr18:30156267-30156616	SK-N-SH_RA	brain:	n/a	chr18:30156439-30156452 chr18:30156436-30156455
7	KAP1	chr18:30156264-30157055	U2OS	brain:	n/a	n/a
8	RAD21	chr18:30156225-30156590	HCT-116	colon:	n/a	chr18:30156439-30156452 chr18:30156436-30156455
9	CTCF	chr18:30156154-30156784	SK-N-SH	brain:	n/a	chr18:30156435-30156453 chr18:30156438-30156451 chr18:30156438-30156447
10	RAD21	chr18:30156337-30156593	MCF-7	breast:	n/a	chr18:30156439-30156452 chr18:30156436-30156455
11	RAD21	chr18:30156170-30156691	MCF-7	breast:	n/a	chr18:30156439-30156452 chr18:30156436-30156455
12	SMC3	chr18:30156358-30156620	Hela-S3	cervix:	n/a	chr18:30156437-30156451
13	RAD21	chr18:30156275-30156645	H1-hESC	embryonic stem cell:	n/a	chr18:30156439-30156452 chr18:30156436-30156455
14	RAD21	chr18:30156189-30156650	HepG2	liver:	n/a	chr18:30156439-30156452 chr18:30156436-30156455
15	CTCF	chr18:30156273-30156583	GM12878	blood:	n/a	chr18:30156435-30156453 chr18:30156438-30156451 chr18:30156438-30156447
16	SMC3	chr18:30156345-30156609	HepG2	liver:	n/a	chr18:30156437-30156451
17	GATA3	chr18:30156427-30156670	SH-SY5Y	brain:	n/a	n/a
18	ZNF143	chr18:30156300-30156583	H1-hESC	embryonic stem cell:	n/a	n/a
19	RAD21	chr18:30156237-30156674	ECC-1	luminal epithelium:	n/a	chr18:30156439-30156452 chr18:30156436-30156455
20	RAD21	chr18:30156317-30156622	H1-hESC	embryonic stem cell:	n/a	chr18:30156439-30156452 chr18:30156436-30156455
21	RAD21	chr18:30156292-30156621	HepG2	liver:	n/a	chr18:30156439-30156452 chr18:30156436-30156455
22	KAP1	chr18:30156270-30156899	HEK293	kidney:	n/a	n/a
23	TAF1	chr18:30156491-30156772	PFSK-1	brain:	n/a	n/a
24	RAD21	chr18:30156212-30156693	SK-N-SH_RA	brain:	n/a	chr18:30156439-30156452 chr18:30156436-30156455
25	CTCF	chr18:30156211-30156635	MCF-7	breast:	n/a	chr18:30156435-30156453 chr18:30156438-30156451 chr18:30156438-30156447

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:30155938..30156890-chr18:30249254..30250445,9	MCF-7	breast:
2	chr18:30156031..30156847-chr18:30254282..30255103,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263688	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs16963576	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16963609	1.00[EUR][1000 genomes]
rs16963616	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56815671	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59047993	1.00[EUR][1000 genomes]
rs7236226	1.00[EUR][1000 genomes]
rs73409218	1.00[EUR][1000 genomes]
rs73409221	1.00[EUR][1000 genomes]
rs73409228	1.00[EUR][1000 genomes]
rs73425647	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73425650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9807156	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv909524	chr18:30115418-30196804	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv909525	chr18:30115418-30215056	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv909526	chr18:30124311-30259109	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1066906	chr18:30125366-30192567	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv543676	chr18:30125366-30192567	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv431976	chr18:30129553-30194102	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:30156200-30156600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr18:30156200-30156800	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr18:30156200-30156800	Enhancers	Fetal Kidney	kidney
4	chr18:30156200-30157400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr18:30156400-30156600	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr18:30156400-30156800	Active TSS	Brain Anterior Caudate	brain
7	chr18:30156400-30156800	Active TSS	Brain Hippocampus Middle	brain
8	chr18:30156400-30157000	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr18:30156400-30157200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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