Variant report

Variant	rs309935
Chromosome Location	chr5:42878462-42878463
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10036147	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10036468	0.89[ASN][1000 genomes]
rs10044301	0.90[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10053947	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10061198	0.89[ASN][1000 genomes]
rs10068961	0.91[ASN][1000 genomes]
rs10072017	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12655096	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12658770	0.86[ASN][1000 genomes]
rs12659760	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13156119	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13354920	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs160330	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs188793	0.94[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1902100	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2098715	0.97[ASN][1000 genomes]
rs2548362	0.80[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2548364	0.83[EUR][1000 genomes]
rs2548365	0.84[EUR][1000 genomes]
rs2548366	0.84[EUR][1000 genomes]
rs2603622	0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2603624	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28415991	0.91[ASN][1000 genomes]
rs309932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309934	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309942	0.81[EUR][1000 genomes]
rs315246	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs315253	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs315262	0.89[YRI][hapmap]
rs315263	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34917335	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34981544	0.89[ASN][1000 genomes]
rs371261	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs378235	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs378344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs388214	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs420550	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs435312	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs446294	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4482913	0.89[ASN][1000 genomes]
rs4513706	0.90[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs453436	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6451649	0.89[ASN][1000 genomes]
rs6451650	0.89[ASN][1000 genomes]
rs6451651	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6451652	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6451653	0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs6451654	0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs6864892	0.97[ASN][1000 genomes]
rs6867854	0.88[ASN][1000 genomes]
rs6875237	0.89[ASN][1000 genomes]
rs6881608	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6885355	0.89[ASN][1000 genomes]
rs6886626	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6895458	0.89[ASN][1000 genomes]
rs6895751	0.89[ASN][1000 genomes]
rs71627562	0.95[ASN][1000 genomes]
rs71627563	0.95[ASN][1000 genomes]
rs7701142	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7721545	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9885101	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][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	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription 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	113 gene(s)	inside rSNPs	diseases
2	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
3	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
5	nsv523033	chr5:42752037-42919685	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv965602	chr5:42767568-42889585	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
8	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
9	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
10	nsv1018276	chr5:42809131-42975245	Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42872600-42882200	Enhancers	Fetal Intestine Large	intestine
2	chr5:42872600-42882400	Enhancers	Fetal Intestine Small	intestine
3	chr5:42875000-42878600	Enhancers	Small Intestine	intestine
4	chr5:42875400-42878800	Flanking Active TSS	HepG2	liver
5	chr5:42876000-42879600	Enhancers	Fetal Stomach	stomach
6	chr5:42876200-42879200	Weak transcription	Lung	lung
7	chr5:42876200-42887200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:42876400-42878600	Enhancers	Colonic Mucosa	Colon
9	chr5:42877000-42878800	Enhancers	Brain Angular Gyrus	brain
10	chr5:42877000-42879200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:42877000-42879800	Enhancers	Duodenum Mucosa	Duodenum
12	chr5:42877000-42879800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr5:42877000-42879800	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr5:42877000-42880400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:42877000-42882000	Enhancers	Liver	Liver
16	chr5:42877200-42878800	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr5:42877200-42879400	Enhancers	Fetal Lung	lung
18	chr5:42877200-42879600	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr5:42877200-42879800	Enhancers	Brain Anterior Caudate	brain
20	chr5:42877200-42879800	Enhancers	Brain Hippocampus Middle	brain
21	chr5:42877200-42879800	Enhancers	Brain Substantia Nigra	brain
22	chr5:42877400-42878800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr5:42877600-42878600	Weak transcription	Ovary	ovary
24	chr5:42877600-42878800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr5:42877600-42882200	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr5:42877800-42887600	Weak transcription	Adipose Nuclei	Adipose
27	chr5:42878200-42878600	Enhancers	Fetal Kidney	kidney
28	chr5:42878400-42879000	Enhancers	Stomach Smooth Muscle	stomach

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