Variant report

Variant	rs56358623
Chromosome Location	chr1:247376513-247376514
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	CEBPB	chr1:247376489-247376846	K562	blood:	n/a	n/a
2	TEAD4	chr1:247376267-247376885	K562	blood:	n/a	n/a
3	EP300	chr1:247376451-247376895	GM12878	blood:	n/a	n/a
4	EP300	chr1:247376463-247376919	K562	blood:	n/a	n/a
5	FOS	chr1:247376502-247377181	MCF10A-Er-Src	breast:	n/a	n/a
6	EP300	chr1:247376487-247376960	GM12878	blood:	n/a	n/a
7	MAFK	chr1:247376161-247376757	HepG2	liver:	n/a	n/a
8	CHD1	chr1:247376497-247376567	GM12878	blood:	n/a	n/a
9	SIN3A	chr1:247376223-247376548	GM12878	blood:	n/a	n/a
10	IRF1	chr1:247376300-247376536	K562	blood:	n/a	n/a
11	RCOR1	chr1:247376370-247376839	GM12878	blood:	n/a	n/a
12	JUND	chr1:247376357-247376908	K562	blood:	n/a	chr1:247376399-247376408 chr1:247376721-247376732
13	MAFK	chr1:247376075-247376745	K562	blood:	n/a	n/a
14	BCL11A	chr1:247376512-247376918	GM12878	blood:	n/a	n/a
15	MAFF	chr1:247376310-247376767	K562	blood:	n/a	n/a
16	ATF3	chr1:247376487-247376893	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:247375650..247377516-chr1:247377910..247380248,2	K562	blood:
2	chr1:247374235..247377046-chr1:247498080..247500631,2	K562	blood:
3	chr1:247375724..247377747-chr1:247379466..247381857,2	K562	blood:

Variant related genes	Relation type
MIR3916	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12083552	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17720872	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41305576	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55876066	0.81[EUR][1000 genomes]
rs55932854	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56036028	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56123640	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56130102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56212015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61087736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72770359	0.89[AMR][1000 genomes]
rs72770361	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72770366	0.96[EUR][1000 genomes]
rs72770367	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72770371	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72770374	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72770379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72770384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72770390	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72770391	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
3	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
4	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
6	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
7	nsv1002438	chr1:247173851-247401380	ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
8	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
9	nsv873436	chr1:247339064-247385877	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247374200-247379600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:247374600-247376800	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr1:247374600-247376800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
4	chr1:247374600-247377200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:247374600-247377200	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr1:247374600-247377200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:247374600-247379600	Weak transcription	Fetal Thymus	thymus
8	chr1:247374800-247377000	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr1:247375000-247377200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:247375200-247376600	Enhancers	HepG2	liver
11	chr1:247375600-247376600	Enhancers	K562	blood
12	chr1:247375600-247377200	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr1:247375800-247376800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr1:247376200-247377200	Enhancers	GM12878-XiMat	blood
15	chr1:247376400-247376600	Enhancers	NHDF-Ad	bronchial
16	chr1:247376400-247376800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links