Variant report

Variant	rs2525539
Chromosome Location	chr7:99545309-99545310
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	SPI1	chr7:99545232-99545602	HL-60	blood:	n/a	chr7:99545425-99545434

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:99544479..99546185-chr7:99557536..99559733,2	K562	blood:
2	chr7:99515531..99518710-chr7:99542097..99545437,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222966	TF binding region
ENSG00000146833	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10267212	0.82[CEU][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap]
rs1076237	0.81[CEU][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap]
rs1865472	0.95[YRI][hapmap]
rs1981549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247762	0.90[YRI][hapmap]
rs2404975	0.97[ASN][1000 genomes]
rs2525535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525536	0.98[ASN][1000 genomes]
rs2525540	0.98[ASN][1000 genomes]
rs2525543	0.98[ASN][1000 genomes]
rs2525545	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525549	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[ASN][1000 genomes]
rs2525550	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2525558	0.97[ASN][1000 genomes]
rs2527887	0.96[ASN][1000 genomes]
rs2527888	0.96[ASN][1000 genomes]
rs2527889	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2527898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2527900	0.95[YRI][hapmap]
rs2527908	0.95[YRI][hapmap]
rs2572000	0.95[YRI][hapmap]
rs2572002	0.94[YRI][hapmap]
rs35656988	0.94[ASN][1000 genomes]
rs6465760	0.82[CEU][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap]
rs7781442	0.95[YRI][hapmap]
rs7801568	1.00[YRI][hapmap]

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	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

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs2525539	TRIM4	cis	multi-tissue	Pritchard
rs2525539	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs2525539	GATS	cis	parietal	SCAN
rs2525539	PILRB	cis	parietal	SCAN
rs2525539	OR2AE1	cis	cerebellum	SCAN
rs2525539	OR2AE1	cis	parietal	SCAN
rs2525539	GNB2	cis	cerebellum	SCAN
rs2525539	TRIM4	cis	Thyroid	GTEx
rs2525539	AP4M1	cis	multi-tissue	Pritchard
rs2525539	TECPR1	cis	cerebellum	SCAN
rs2525539	GATS	cis	multi-tissue	Pritchard
rs2525539	GATS	cis	cerebellum	SCAN
rs2525539	PILRB	cis	multi-tissue	Pritchard
rs2525539	NAPEPLD	cis	parietal	SCAN
rs2525539	ZSCAN21	cis	parietal	SCAN
rs2525539	LMTK2	cis	cerebellum	SCAN
rs2525539	SERPINE1	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99532400-99548000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:99543000-99545600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr7:99543200-99547400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:99545200-99545400	Enhancers	H9 Cell Line	embryonic stem cell
5	chr7:99545200-99545600	Enhancers	Gastric	stomach
6	chr7:99545200-99545800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr7:99545200-99545800	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr7:99545200-99546400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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