Variant report

Variant	rs969303
Chromosome Location	chr2:56466834-56466835
allele	A/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	GATA3	chr2:56466267-56467290	SK-N-SH	brain:	n/a	chr2:56466345-56466352
2	JUND	chr2:56466303-56467207	SK-N-SH	brain:	n/a	chr2:56466627-56466639
3	FOSL2	chr2:56466346-56466988	SK-N-SH	brain:	n/a	chr2:56466627-56466639
4	TCF12	chr2:56466393-56467289	SK-N-SH	brain:	n/a	n/a
5	PBX3	chr2:56466428-56467041	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr2:56466467-56467049	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr2:56466371-56467243	SK-N-SH	brain:	n/a	n/a
8	TCF12	chr2:56466249-56467231	SK-N-SH	brain:	n/a	n/a
9	PBX3	chr2:56466326-56467159	SK-N-SH	brain:	n/a	n/a
10	EP300	chr2:56466410-56467068	SK-N-SH_RA	brain:	n/a	n/a
11	EP300	chr2:56466348-56467193	SK-N-SH	brain:	n/a	n/a
12	JUND	chr2:56466439-56467066	SK-N-SH	brain:	n/a	chr2:56466627-56466639
13	FOS	chr2:56466614-56466879	HUVEC	blood vessel:	n/a	chr2:56466627-56466639 chr2:56466737-56466748
14	EP300	chr2:56465943-56467199	SK-N-SH	brain:	n/a	n/a
15	NFIC	chr2:56466268-56467172	SK-N-SH	brain:	n/a	n/a
16	JUND	chr2:56466326-56467078	SK-N-SH	brain:	n/a	chr2:56466627-56466639
17	RAD21	chr2:56466427-56466837	SK-N-SH_RA	brain:	n/a	n/a
18	RAD21	chr2:56466480-56467028	SK-N-SH_RA	brain:	n/a	n/a
19	POLR2A	chr2:56466485-56466940	SK-N-SH	brain:	n/a	n/a
20	EP300	chr2:56466406-56467159	SK-N-SH_RA	brain:	n/a	n/a
21	FOXM1	chr2:56466385-56467056	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
RNA5SP93	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1001471	0.85[JPT][hapmap]
rs10188465	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10490397	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11125618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12613716	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12623053	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12623278	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12713316	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12993884	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12994087	0.89[ASN][1000 genomes]
rs12996636	0.90[CHB][hapmap]
rs13004757	0.90[JPT][hapmap]
rs13012528	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs13016868	0.90[JPT][hapmap]
rs13025817	0.91[JPT][hapmap]
rs13403828	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs13429808	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1468914	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17047656	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs17047684	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs17047705	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2111476	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2193485	0.91[JPT][hapmap]
rs2216325	0.90[CHB][hapmap]
rs2216332	0.90[JPT][hapmap]
rs35637593	0.90[ASN][1000 genomes]
rs3971875	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6710311	0.90[CHB][hapmap]
rs6730327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563888	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7576428	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7588401	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7590310	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7591193	0.90[ASN][1000 genomes]
rs7591392	0.90[ASN][1000 genomes]
rs759615	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs7602551	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9653542	0.90[ASN][1000 genomes]
rs969301	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs969302	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[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	esv2757799	chr2:56178439-56472394	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2759051	chr2:56178439-56472394	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	nsv874162	chr2:56255832-56480571	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv874169	chr2:56383762-56473480	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv530516	chr2:56447922-56633505	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56465800-56467600	Enhancers	Muscle Satellite Cultured Cells	--
2	chr2:56466000-56467400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:56466600-56472000	Weak transcription	HSMM	muscle
4	chr2:56466800-56469800	Weak transcription	HUVEC	blood vessel

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