Variant report

Variant	rs2525542
Chromosome Location	chr7:99548569-99548570
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	CBX3	chr7:99548473-99548806	HCT-116	colon:	n/a	n/a
2	TRIM28	chr7:99548510-99548738	K562	blood:	n/a	n/a
3	SETDB1	chr7:99548315-99548810	U2OS	brain:	n/a	n/a
4	ZNF143	chr7:99548462-99548734	H1-hESC	embryonic stem cell:	n/a	n/a
5	KAP1	chr7:99548296-99548904	K562	blood:	n/a	n/a
6	TRIM28	chr7:99548356-99548837	K562	blood:	n/a	n/a
7	CBX3	chr7:99548435-99548808	K562	blood:	n/a	n/a
8	CBX3	chr7:99548459-99548786	K562	blood:	n/a	n/a
9	ZNF143	chr7:99548535-99548676	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:99546378..99548989-chr7:99551538..99554041,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222966	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs10808114	0.81[EUR][1000 genomes]
rs1981548	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2057766	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2107351	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2247761	0.81[EUR][1000 genomes]
rs2525534	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525537	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525541	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525547	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2525548	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2527886	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527890	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527891	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527892	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527893	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527894	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527895	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527897	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527899	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2527901	0.81[EUR][1000 genomes]
rs2527903	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2527906	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2527909	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2527913	0.81[EUR][1000 genomes]
rs2527914	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2527915	0.81[EUR][1000 genomes]
rs2527921	0.81[EUR][1000 genomes]
rs2527922	0.81[EUR][1000 genomes]
rs2571992	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2571993	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2571994	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2571996	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2571997	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2571998	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2571999	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2572003	0.81[EUR][1000 genomes]
rs2572005	0.81[EUR][1000 genomes]
rs2572006	0.81[EUR][1000 genomes]
rs2572008	0.81[EUR][1000 genomes]
rs7809747	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv607930	chr7:99525241-99602191	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv1828362	chr7:99530233-99628773	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv888772	chr7:99533178-99602191	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv1830255	chr7:99544908-99626331	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	esv1832985	chr7:99546856-99615911	Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2525542	TRIM4	cis	Nerve Tibial	GTEx
rs2525542	TRIM4	cis	Esophagus Muscularis	GTEx
rs2525542	TRIM4	cis	Whole Blood	GTEx
rs2525542	TRIM4	cis	lung	GTEx
rs2525542	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs2525542	TRIM4	cis	Skin Sun Exposed Lower leg	GTEx
rs2525542	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs2525542	TRIM4	cis	Artery Tibial	GTEx
rs2525542	TRIM4	cis	Muscle Skeletal	GTEx
rs2525542	TRIM4	cis	Stomach	GTEx
rs2525542	TRIM4	cis	Adipose Subcutaneous	GTEx
rs2525542	TRIM4	cis	Artery Aorta	GTEx
rs2525542	TRIM4	cis	Thyroid	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99546400-99552800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr7:99548000-99548800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

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