Variant report

Variant	rs2133716
Chromosome Location	chr5:177095517-177095518
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10036396	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10040391	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10063842	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1047577	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11249619	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12654617	0.86[ASN][1000 genomes]
rs13164561	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1696858	0.81[GIH][hapmap];0.80[TSI][hapmap]
rs17832583	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1872623	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1963011	0.89[ASN][1000 genomes]
rs2334991	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2650285	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28375402	0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap]
rs34327383	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.89[ASN][1000 genomes]
rs3965330	0.87[ASN][1000 genomes]
rs4458584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56981142	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs59542146	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6600950	0.91[JPT][hapmap]
rs6882209	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6886539	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.85[ASN][1000 genomes]
rs6889184	0.91[ASN][1000 genomes]
rs7703727	0.91[ASN][1000 genomes]
rs7708299	0.93[ASN][1000 genomes]
rs7731783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024444	chr5:176751921-177427715	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	142 gene(s)	inside rSNPs	diseases
2	esv2752795	chr5:176898619-177488281	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv883182	chr5:176980995-177322056	Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv969021	chr5:177060702-177111251	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2133716	RP11-1101H11.1	cis	Heart Left Ventricle	GTEx
rs2133716	B4GALT7	cis	Whole Blood	GTEx
rs2133716	B4GALT7	cis	lymphoblastoid	seeQTL
rs2133716	FAM153A	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177054400-177096000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr5:177076800-177098200	Weak transcription	Fetal Stomach	stomach
3	chr5:177077000-177098200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:177092400-177096600	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr5:177092400-177096800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:177094200-177098200	Weak transcription	Ovary	ovary
7	chr5:177095400-177095600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:177095400-177095600	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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