Variant report

Variant	rs7729853
Chromosome Location	chr5:58959977-58959978
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10036621	1.00[EUR][1000 genomes]
rs10037195	1.00[EUR][1000 genomes]
rs10070270	1.00[EUR][1000 genomes]
rs10076058	1.00[EUR][1000 genomes]
rs10078146	1.00[EUR][1000 genomes]
rs10214307	1.00[EUR][1000 genomes]
rs10472115	1.00[EUR][1000 genomes]
rs10514882	1.00[EUR][1000 genomes]
rs16890137	1.00[EUR][1000 genomes]
rs16890246	1.00[EUR][1000 genomes]
rs16890279	1.00[EUR][1000 genomes]
rs16890284	1.00[EUR][1000 genomes]
rs16890314	1.00[EUR][1000 genomes]
rs2016004	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3797208	0.82[LWK][hapmap];0.92[MKK][hapmap];1.00[EUR][1000 genomes]
rs4602573	1.00[EUR][1000 genomes]
rs55641022	1.00[EUR][1000 genomes]
rs55720412	1.00[EUR][1000 genomes]
rs55930874	1.00[EUR][1000 genomes]
rs56203004	1.00[EUR][1000 genomes]
rs57153097	1.00[EUR][1000 genomes]
rs57402847	1.00[EUR][1000 genomes]
rs57413746	1.00[EUR][1000 genomes]
rs57434558	1.00[EUR][1000 genomes]
rs57438370	1.00[EUR][1000 genomes]
rs57465219	1.00[EUR][1000 genomes]
rs57742530	1.00[EUR][1000 genomes]
rs58746465	1.00[EUR][1000 genomes]
rs58815573	1.00[EUR][1000 genomes]
rs59025824	1.00[EUR][1000 genomes]
rs60774517	1.00[EUR][1000 genomes]
rs61146095	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6450533	1.00[EUR][1000 genomes]
rs6450534	1.00[EUR][1000 genomes]
rs6650953	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6861008	1.00[EUR][1000 genomes]
rs6861209	1.00[EUR][1000 genomes]
rs6862255	1.00[EUR][1000 genomes]
rs6866277	1.00[EUR][1000 genomes]
rs6867150	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6869978	1.00[EUR][1000 genomes]
rs6873715	1.00[EUR][1000 genomes]
rs6873774	1.00[EUR][1000 genomes]
rs6874354	1.00[EUR][1000 genomes]
rs6874831	1.00[EUR][1000 genomes]
rs6876534	1.00[EUR][1000 genomes]
rs6878243	0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs6882607	0.96[YRI][hapmap];0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6885868	1.00[EUR][1000 genomes]
rs6888341	1.00[EUR][1000 genomes]
rs6889471	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6891000	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6893381	1.00[EUR][1000 genomes]
rs6895425	0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs6896644	1.00[EUR][1000 genomes]
rs6896871	1.00[EUR][1000 genomes]
rs73092839	1.00[EUR][1000 genomes]
rs73092846	1.00[EUR][1000 genomes]
rs73758838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73758839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73758847	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73758848	0.80[AFR][1000 genomes]
rs73758850	1.00[EUR][1000 genomes]
rs73758851	1.00[EUR][1000 genomes]
rs73758856	1.00[EUR][1000 genomes]
rs73758857	1.00[EUR][1000 genomes]
rs73758858	1.00[EUR][1000 genomes]
rs73758859	1.00[EUR][1000 genomes]
rs73758860	1.00[EUR][1000 genomes]
rs73758862	1.00[EUR][1000 genomes]
rs73758864	1.00[EUR][1000 genomes]
rs73758867	1.00[EUR][1000 genomes]
rs73758868	1.00[EUR][1000 genomes]
rs73761012	1.00[EUR][1000 genomes]
rs7703935	0.89[ASW][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap];0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs7705119	1.00[EUR][1000 genomes]
rs7705820	1.00[EUR][1000 genomes]
rs7707756	1.00[EUR][1000 genomes]
rs7707855	0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7708246	1.00[EUR][1000 genomes]
rs7709094	1.00[EUR][1000 genomes]
rs7709292	1.00[EUR][1000 genomes]
rs7710349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7711022	1.00[EUR][1000 genomes]
rs7713509	1.00[EUR][1000 genomes]
rs7713964	0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs7716837	0.87[LWK][hapmap];0.97[MKK][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7723356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7727677	1.00[EUR][1000 genomes]
rs7728346	1.00[EUR][1000 genomes]
rs7729112	1.00[EUR][1000 genomes]
rs7734202	1.00[EUR][1000 genomes]
rs7737029	1.00[EUR][1000 genomes]
rs7737211	1.00[EUR][1000 genomes]
rs9292215	1.00[EUR][1000 genomes]
rs9292216	1.00[EUR][1000 genomes]
rs9292217	1.00[EUR][1000 genomes]
rs9765834	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	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv427720	chr5:58913581-59086987	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv462190	chr5:58936943-59023870	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv598258	chr5:58936943-59023870	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1034283	chr5:58940594-59040762	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv537767	chr5:58940594-59040762	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58948000-58961600	Weak transcription	Gastric	stomach
2	chr5:58957400-58960800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr5:58958000-58961400	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr5:58958200-58960600	Weak transcription	Brain Hippocampus Middle	brain
5	chr5:58958200-58961600	Weak transcription	Psoas Muscle	Psoas
6	chr5:58958200-58964000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:58958400-58960000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:58958400-58960800	Weak transcription	Adipose Nuclei	Adipose
9	chr5:58958400-58960800	Weak transcription	HepG2	liver
10	chr5:58958400-58962400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr5:58958400-58962400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr5:58958400-58962600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr5:58958400-58974400	Weak transcription	Fetal Intestine Small	intestine
14	chr5:58958600-58961000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:58958600-58961000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr5:58958600-58961000	Weak transcription	Fetal Lung	lung
17	chr5:58958600-58961000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr5:58958600-58961400	Weak transcription	Stomach Mucosa	stomach
19	chr5:58959000-58960800	Weak transcription	Liver	Liver
20	chr5:58959000-58962600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:58959000-58963200	Enhancers	A549	lung
22	chr5:58959600-58961200	Enhancers	Colon Smooth Muscle	Colon
23	chr5:58959600-58962600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:58959600-58962600	Enhancers	Hela-S3	cervix
25	chr5:58959600-58970400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:58959800-58960400	Enhancers	Pancreatic Islets	Pancreatic Islet

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