Variant report

Variant	rs2527886
Chromosome Location	chr7:99552168-99552169
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99546378..99548989-chr7:99551538..99554041,2	MCF-7	breast:
2	chr7:99550695..99553534-chr7:99558845..99560540,2	MCF-7	breast:
3	chr7:99552086..99554197-chr7:99560760..99564029,3	MCF-7	breast:
4	chr16:3072904..3075257-chr7:99551706..99553216,2	MCF-7	breast:
5	chr7:99515983..99517855-chr7:99552009..99553690,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103145	Chromatin interaction
ENSG00000131652	Chromatin interaction
ENSG00000146833	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1025576	0.81[MKK][hapmap]
rs1048705	0.84[CHB][hapmap]
rs10808114	0.84[CHB][hapmap]
rs1981548	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2057766	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2060452	0.82[CHB][hapmap]
rs2082744	0.83[MKK][hapmap]
rs2107351	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2247761	0.84[CHB][hapmap]
rs2525534	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525542	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525547	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525548	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2527890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527891	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527892	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2527894	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2527895	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2527897	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2527899	0.84[CHB][hapmap];0.83[MKK][hapmap]
rs2527901	0.84[CHB][hapmap]
rs2527903	0.84[CHB][hapmap];0.85[MKK][hapmap]
rs2527907	0.84[CHB][hapmap]
rs2527914	0.84[CHB][hapmap]
rs2527918	0.82[CHB][hapmap]
rs2527919	0.84[CHB][hapmap]
rs2527922	0.84[CHB][hapmap]
rs2571992	0.84[CHB][hapmap]
rs2571997	0.84[CHB][hapmap]
rs2571998	0.84[CHB][hapmap]
rs2572003	0.84[CHB][hapmap]
rs2572005	0.84[CHB][hapmap]
rs2572006	0.84[CHB][hapmap]
rs2572008	0.84[CHB][hapmap]
rs2572009	0.85[MKK][hapmap]
rs2572010	0.84[CHB][hapmap]
rs2572022	0.81[MKK][hapmap]
rs6962405	0.80[GIH][hapmap]

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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs2527886	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs2527886	TRIM4	cis	Stomach	GTEx
rs2527886	TRIM4	cis	Nerve Tibial	GTEx
rs2527886	TRIM4	cis	Skin Sun Exposed Lower leg	GTEx
rs2527886	TRIM4	cis	multi-tissue	Pritchard
rs2527886	TRIM4	cis	Esophagus Muscularis	GTEx
rs2527886	TRIM4	cis	parietal	SCAN
rs2527886	TRIM4	cis	cerebellum	SCAN
rs2527886	TRIM4	cis	Artery Aorta	GTEx
rs2527886	OR2AE1	cis	cerebellum	SCAN
rs2527886	OR2AE1	cis	parietal	SCAN
rs2527886	TRIM4	cis	Adipose Subcutaneous	GTEx
rs2527886	TRIM4	cis	Artery Tibial	GTEx
rs2527886	TRIM4	cis	Muscle Skeletal	GTEx
rs2527886	TRIM4	cis	normal skin	skin_eQTL
rs2527886	TRIM4	cis	Thyroid	GTEx
rs2527886	PILRB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 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	chr7:99550400-99553800	Enhancers	Liver	Liver
3	chr7:99550800-99553200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr7:99551000-99552200	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr7:99551400-99552800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:99551400-99552800	Weak transcription	HepG2	liver
7	chr7:99551600-99552200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr7:99551800-99552400	Enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links