Variant report

Variant	rs1027109
Chromosome Location	chr4:56460493-56460494
allele	C/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	POLR2A	chr4:56459602-56461000	K562	blood:	n/a	n/a
2	POLR2A	chr4:56460274-56461020	K562	blood:	n/a	n/a
3	POLR2A	chr4:56457051-56461679	K562	blood:	n/a	n/a
4	POLR2A	chr4:56457732-56460674	K562	blood:	n/a	n/a
5	BCL3	chr4:56459850-56460592	K562	blood:	n/a	chr4:56460261-56460270
6	POLR2A	chr4:56460308-56460956	K562	blood:	n/a	n/a
7	POLR2A	chr4:56460211-56461092	K562	blood:	n/a	n/a
8	POLR2A	chr4:56458002-56460867	K562	blood:	n/a	n/a
9	CCNT2	chr4:56460410-56460923	K562	blood:	n/a	n/a
10	POLR2A	chr4:56458085-56461042	K562	blood:	n/a	n/a
11	POLR2A	chr4:56458216-56461090	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:56459697..56462267-chr4:56481406..56483258,2	K562	blood:
2	chr4:56459163..56461447-chr4:56461922..56464276,2	K562	blood:
3	chr4:56459983..56461740-chr4:56464229..56467052,3	K562	blood:

Variant related genes	Relation type
PDCL2	TF binding region

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10018565	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10022874	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10866426	0.90[EUR][1000 genomes]
rs13139886	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1387198	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1471981	0.90[EUR][1000 genomes]
rs1552524	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1906674	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1906678	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1963566	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2101473	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2101474	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2412667	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4865019	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59494560	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61541312	0.90[EUR][1000 genomes]
rs6554294	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6554295	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6554296	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6843720	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7657199	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7659330	0.82[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7662646	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7681959	0.81[AMR][1000 genomes];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	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv998179	chr4:56425126-56694339	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv932636	chr4:56438618-56667329	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 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	chr4:56441200-56464400	Weak transcription	K562	blood
2	chr4:56458600-56463800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:56460000-56464800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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