Variant report

Variant	rs7933339
Chromosome Location	chr11:58658875-58658876
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:58345930..58347450-chr11:58657978..58660327,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLYAT-1	chr11:58657761-58659741	l_477_chr11:58656260-58660325_ovary

Variant related genes	Relation type
ENSG00000255073	Chromatin interaction
ENSG00000186660	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10750905	0.89[AFR][1000 genomes]
rs10792188	0.86[AFR][1000 genomes]
rs10792189	0.86[AFR][1000 genomes]
rs10792203	0.88[AFR][1000 genomes]
rs12575251	0.80[EUR][1000 genomes]
rs1943286	0.84[AFR][1000 genomes]
rs1943287	0.86[AFR][1000 genomes]
rs1943288	0.86[AFR][1000 genomes]
rs1943289	0.82[AFR][1000 genomes]
rs1943290	0.86[AFR][1000 genomes]
rs1943291	0.86[AFR][1000 genomes]
rs1943292	0.86[AFR][1000 genomes]
rs1943293	0.86[AFR][1000 genomes]
rs1943294	0.83[AFR][1000 genomes]
rs1943295	0.83[AFR][1000 genomes]
rs1943296	0.83[AFR][1000 genomes]
rs1943297	0.86[AFR][1000 genomes]
rs1943298	0.86[AFR][1000 genomes]
rs1943300	0.88[AFR][1000 genomes]
rs1943301	0.92[AFR][1000 genomes]
rs1943302	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1943306	0.95[AFR][1000 genomes]
rs2156350	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2156351	0.95[AFR][1000 genomes]
rs2187269	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2212850	0.92[AFR][1000 genomes]
rs2226794	0.92[AFR][1000 genomes]
rs2849855	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2856259	0.86[AFR][1000 genomes]
rs3020907	0.82[AFR][1000 genomes]
rs3020908	0.86[AFR][1000 genomes]
rs3020909	0.86[AFR][1000 genomes]
rs4103678	0.86[AFR][1000 genomes]
rs488093	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs490828	0.89[AFR][1000 genomes]
rs492802	0.86[AFR][1000 genomes]
rs493580	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs493659	0.86[AFR][1000 genomes]
rs4939234	0.94[AFR][1000 genomes]
rs4939236	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4939237	0.92[AFR][1000 genomes]
rs4939238	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs496601	0.86[AFR][1000 genomes]
rs497348	0.86[AFR][1000 genomes]
rs512832	0.86[AFR][1000 genomes]
rs513590	0.86[AFR][1000 genomes]
rs518089	0.86[AFR][1000 genomes]
rs519043	0.86[AFR][1000 genomes]
rs519256	0.86[AFR][1000 genomes]
rs519310	0.86[AFR][1000 genomes]
rs521781	0.89[AFR][1000 genomes]
rs524689	0.88[AFR][1000 genomes]
rs526640	0.88[AFR][1000 genomes]
rs529734	0.86[AFR][1000 genomes]
rs531737	0.86[AFR][1000 genomes]
rs533438	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs535234	0.86[AFR][1000 genomes]
rs537098	0.85[AFR][1000 genomes]
rs545803	0.86[AFR][1000 genomes]
rs547469	0.86[AFR][1000 genomes]
rs547540	0.95[AFR][1000 genomes]
rs549519	0.94[AFR][1000 genomes]
rs550272	0.83[ASN][1000 genomes]
rs550275	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs552887	0.89[AFR][1000 genomes]
rs557895	0.86[AFR][1000 genomes]
rs558013	0.86[AFR][1000 genomes]
rs558099	0.83[AFR][1000 genomes]
rs558146	0.86[AFR][1000 genomes]
rs558403	0.87[AFR][1000 genomes]
rs560816	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs561676	0.86[AFR][1000 genomes]
rs563687	0.86[AFR][1000 genomes]
rs564570	0.86[AFR][1000 genomes]
rs567460	0.89[AFR][1000 genomes]
rs570835	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs574497	0.82[AFR][1000 genomes]
rs576050	0.86[AFR][1000 genomes]
rs587953	0.86[AFR][1000 genomes]
rs591856	0.89[AFR][1000 genomes]
rs592308	0.89[AFR][1000 genomes]
rs593537	0.81[AFR][1000 genomes]
rs598767	0.86[AFR][1000 genomes]
rs599254	0.86[AFR][1000 genomes]
rs599275	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs600215	0.86[AFR][1000 genomes]
rs600559	0.89[AFR][1000 genomes]
rs605870	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs608043	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs614365	0.86[AFR][1000 genomes]
rs615237	0.86[AFR][1000 genomes]
rs615781	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs618527	0.84[ASN][1000 genomes]
rs620633	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs621584	0.89[AFR][1000 genomes]
rs628312	0.86[AFR][1000 genomes]
rs630551	0.86[AFR][1000 genomes]
rs631452	0.86[AFR][1000 genomes]
rs635588	0.89[AFR][1000 genomes]
rs642957	0.86[AFR][1000 genomes]
rs643881	0.86[AFR][1000 genomes]
rs644238	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs644312	0.86[AFR][1000 genomes]
rs645667	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs651936	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs657792	0.86[AFR][1000 genomes]
rs658309	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6591499	0.85[AMR][1000 genomes]
rs665148	0.89[AFR][1000 genomes]
rs667889	0.88[AFR][1000 genomes]
rs668254	0.88[AFR][1000 genomes]
rs678346	0.86[AFR][1000 genomes]
rs678727	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs678880	0.86[AFR][1000 genomes]
rs679551	0.88[AFR][1000 genomes]
rs679625	1.00[JPT][hapmap]
rs680053	0.88[AFR][1000 genomes]
rs680976	0.88[AFR][1000 genomes]
rs682357	0.86[AFR][1000 genomes]
rs682780	0.86[AFR][1000 genomes]
rs7116544	1.00[CEU][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1048605	chr11:58534660-58672438	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1045858	chr11:58547772-58674568	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1052173	chr11:58553516-58678496	Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv3444895	chr11:58614102-58779384	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	esv1824025	chr11:58626835-58669877	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv1831269	chr11:58626835-58669877	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv3445007	chr11:58638330-58709867	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58635000-58668000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:58651000-58671200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr11:58651400-58660200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:58653200-58661400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr11:58658000-58667600	Weak transcription	Brain Germinal Matrix	brain
6	chr11:58658400-58668000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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