Variant report

Variant	rs1553477
Chromosome Location	chr5:53116966-53116967
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	EP300	chr5:53115933-53117020	GM12878	blood:	n/a	chr5:53116805-53116814 chr5:53116372-53116386
2	PAX5	chr5:53116639-53116999	GM12878	blood:	n/a	n/a
3	EP300	chr5:53115987-53117080	GM12878	blood:	n/a	chr5:53116805-53116814 chr5:53116372-53116386
4	POU2F2	chr5:53116398-53117108	GM12878	blood:	n/a	chr5:53116496-53116511 chr5:53116854-53116863 chr5:53116851-53116865 chr5:53116855-53116862 chr5:53116852-53116863 chr5:53116853-53116863
5	POU2F2	chr5:53116608-53117000	GM12891	blood:	n/a	chr5:53116854-53116863 chr5:53116851-53116865 chr5:53116855-53116862 chr5:53116852-53116863 chr5:53116853-53116863
6	BATF	chr5:53116584-53116990	GM12878	blood:	n/a	chr5:53116805-53116816
7	ATF2	chr5:53116530-53117074	GM12878	blood:	n/a	n/a
8	PAX5	chr5:53116633-53116987	GM12878	blood:	n/a	n/a
9	IRF4	chr5:53116514-53117034	GM12878	blood:	n/a	n/a
10	FOS	chr5:53116666-53116984	MCF10A-Er-Src	breast:	n/a	chr5:53116805-53116813 chr5:53116805-53116812 chr5:53116804-53116814
11	BHLHE40	chr5:53115962-53117009	GM12878	blood:	n/a	n/a
12	NFIC	chr5:53116454-53116977	GM12878	blood:	n/a	n/a
13	IKZF1	chr5:53115887-53117035	GM12878	blood:	n/a	n/a
14	POU2F2	chr5:53116606-53117124	GM12891	blood:	n/a	chr5:53116854-53116863 chr5:53116851-53116865 chr5:53116855-53116862 chr5:53116852-53116863 chr5:53116853-53116863
15	POU2F2	chr5:53116589-53117024	GM12878	blood:	n/a	chr5:53116854-53116863 chr5:53116851-53116865 chr5:53116855-53116862 chr5:53116852-53116863 chr5:53116853-53116863
16	TBL1XR1	chr5:53115990-53117017	GM12878	blood:	n/a	n/a
17	STAT1	chr5:53116709-53117047	GM12878	blood:	n/a	chr5:53116805-53116814 chr5:53116804-53116813
18	RUNX3	chr5:53116453-53116977	GM12878	blood:	n/a	n/a
19	MTA3	chr5:53116508-53117060	GM12878	blood:	n/a	n/a
20	RCOR1	chr5:53116075-53116978	GM12878	blood:	n/a	n/a
21	EBF1	chr5:53115898-53117016	GM12878	blood:	n/a	n/a
22	RELA	chr5:53116026-53117034	GM12878	blood:	n/a	n/a
23	EBF1	chr5:53116611-53116992	GM12878	blood:	n/a	n/a
24	PAX5	chr5:53116473-53117089	GM12878	blood:	n/a	chr5:53116538-53116547

Variant related genes	Relation type
ENSG00000250447	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10072767	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1504212	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17248426	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1994870	0.99[ASN][1000 genomes]
rs2007701	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047060	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2047061	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6865692	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6866551	0.99[ASN][1000 genomes]
rs6871876	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872373	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6875907	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7447502	0.84[ASN][1000 genomes]
rs7729718	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1032504	chr5:52908394-53398435	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv537763	chr5:52908394-53398435	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv830298	chr5:52973912-53193398	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv533778	chr5:53092696-53284566	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1019194	chr5:53104869-53178957	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53114800-53117600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:53115200-53121200	Weak transcription	Fetal Muscle Leg	muscle
3	chr5:53116400-53117200	Flanking Active TSS	GM12878-XiMat	blood

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