Variant report

Variant	rs7730188
Chromosome Location	chr5:49877896-49877897
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11952107	1.00[AMR][1000 genomes]
rs11954064	0.94[AMR][1000 genomes]
rs11955651	1.00[AMR][1000 genomes]
rs11959326	1.00[AMR][1000 genomes]
rs13153852	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13155662	0.83[AMR][1000 genomes]
rs13156735	1.00[AMR][1000 genomes]
rs13157079	1.00[AMR][1000 genomes]
rs13157952	0.82[EUR][1000 genomes]
rs13159239	1.00[AMR][1000 genomes]
rs13159553	0.89[EUR][1000 genomes]
rs13162663	0.80[EUR][1000 genomes]
rs13162738	0.94[AMR][1000 genomes]
rs13167408	0.89[EUR][1000 genomes]
rs13169200	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13171248	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13172426	0.98[EUR][1000 genomes]
rs13172836	0.89[EUR][1000 genomes]
rs13174498	1.00[AMR][1000 genomes]
rs13180485	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13180506	0.89[EUR][1000 genomes]
rs13181031	0.94[AMR][1000 genomes]
rs13181117	1.00[AMR][1000 genomes]
rs13183686	0.89[EUR][1000 genomes]
rs13183910	1.00[AMR][1000 genomes]
rs13186653	1.00[AMR][1000 genomes]
rs13190144	1.00[AMR][1000 genomes]
rs1968637	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2354531	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34002233	0.94[AFR][1000 genomes]
rs34183555	0.83[AMR][1000 genomes]
rs34264957	1.00[AMR][1000 genomes]
rs34414061	1.00[AMR][1000 genomes]
rs34443769	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34677483	1.00[AMR][1000 genomes]
rs34827507	1.00[AMR][1000 genomes]
rs35128589	1.00[AMR][1000 genomes]
rs35210389	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35292338	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35347195	1.00[AMR][1000 genomes]
rs35434227	0.89[EUR][1000 genomes]
rs35473824	1.00[AMR][1000 genomes]
rs35596019	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36187734	0.89[EUR][1000 genomes]
rs6859621	1.00[AMR][1000 genomes]
rs6864439	0.91[AFR][1000 genomes]
rs6880398	1.00[AMR][1000 genomes]
rs6892149	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71615974	0.89[EUR][1000 genomes]
rs71615975	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71615978	1.00[AMR][1000 genomes]
rs71615981	0.94[AMR][1000 genomes]
rs71615984	1.00[AMR][1000 genomes]
rs71631479	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71631481	0.98[EUR][1000 genomes]
rs73095026	0.85[AFR][1000 genomes]
rs7711920	0.94[AFR][1000 genomes]
rs7717073	1.00[AMR][1000 genomes]
rs7723395	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7726225	1.00[AMR][1000 genomes]
rs7733931	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032003	chr5:49455624-49881491	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	esv2757995	chr5:49748352-50058182	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv2759342	chr5:49748352-50058182	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7730188	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49873200-49878000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr5:49876800-49891400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:49877400-49884000	Weak transcription	Placenta Amnion	Placenta Amnion

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