Variant report

Variant	rs427799
Chromosome Location	chr5:42877570-42877571
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:42876153..42877710-chr5:42880139..42881887,2	K562	blood:
2	chr5:42874819..42877698-chr5:42883856..42886524,3	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs13361827	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs160331	0.88[CEU][hapmap];0.98[EUR][1000 genomes]
rs160332	0.96[EUR][1000 genomes]
rs16874465	0.94[EUR][1000 genomes]
rs2444853	0.86[EUR][1000 genomes]
rs2548363	0.90[EUR][1000 genomes]
rs2548367	0.84[EUR][1000 genomes]
rs2548368	1.00[CHD][hapmap];0.82[EUR][1000 genomes]
rs2603635	0.84[EUR][1000 genomes]
rs2924818	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs309915	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs309917	1.00[ASN][1000 genomes]
rs309918	1.00[ASN][1000 genomes]
rs309920	0.92[EUR][1000 genomes]
rs309928	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs309933	0.88[CEU][hapmap];0.98[EUR][1000 genomes]
rs309937	0.98[EUR][1000 genomes]
rs309943	0.82[EUR][1000 genomes]
rs309944	0.82[EUR][1000 genomes]
rs309945	0.82[EUR][1000 genomes]
rs315247	0.98[EUR][1000 genomes]
rs315248	0.98[EUR][1000 genomes]
rs315259	0.86[CEU][hapmap];0.98[EUR][1000 genomes]
rs315261	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs315265	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs315267	0.98[EUR][1000 genomes]
rs315268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs315269	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs371686	1.00[ASN][1000 genomes]
rs375476	0.98[EUR][1000 genomes]
rs377822	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378886	0.94[EUR][1000 genomes]
rs387180	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs388377	0.98[EUR][1000 genomes]
rs399923	0.98[EUR][1000 genomes]
rs401102	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs401583	0.98[EUR][1000 genomes]
rs404899	0.98[EUR][1000 genomes]
rs408180	0.98[EUR][1000 genomes]
rs410225	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs424862	0.98[EUR][1000 genomes]
rs426335	0.88[CEU][hapmap];0.98[EUR][1000 genomes]
rs435255	0.98[EUR][1000 genomes]
rs435445	0.98[EUR][1000 genomes]
rs55981030	0.98[EUR][1000 genomes]
rs72759052	0.98[EUR][1000 genomes]
rs72759059	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72759060	0.94[EUR][1000 genomes]
rs72759061	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72759062	0.94[EUR][1000 genomes]
rs72759066	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72759067	0.94[EUR][1000 genomes]
rs72759071	0.92[EUR][1000 genomes]
rs72759072	0.92[EUR][1000 genomes]
rs72759073	0.92[EUR][1000 genomes]
rs72759075	0.92[EUR][1000 genomes]
rs72759077	0.92[EUR][1000 genomes]
rs72759084	0.92[EUR][1000 genomes]
rs72759085	0.90[EUR][1000 genomes]
rs72759086	0.90[EUR][1000 genomes]
rs72759087	0.86[EUR][1000 genomes]
rs72759093	0.82[EUR][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:36 , 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	chr5:42876600-42877600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
10	chr5:42877000-42877600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:42877000-42877600	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr5:42877000-42877600	Enhancers	Ovary	ovary
13	chr5:42877000-42877600	Enhancers	Right Atrium	heart
14	chr5:42877000-42877800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:42877000-42877800	Enhancers	Adipose Nuclei	Adipose
16	chr5:42877000-42878000	Enhancers	K562	blood
17	chr5:42877000-42878200	Weak transcription	Fetal Kidney	kidney
18	chr5:42877000-42878400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr5:42877000-42878800	Enhancers	Brain Angular Gyrus	brain
20	chr5:42877000-42879200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:42877000-42879800	Enhancers	Duodenum Mucosa	Duodenum
22	chr5:42877000-42879800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr5:42877000-42879800	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr5:42877000-42880400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:42877000-42882000	Enhancers	Liver	Liver
26	chr5:42877200-42877600	Active TSS	Brain Cingulate Gyrus	brain
27	chr5:42877200-42877600	Enhancers	Placenta	Placenta
28	chr5:42877200-42877800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:42877200-42878800	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr5:42877200-42879400	Enhancers	Fetal Lung	lung
31	chr5:42877200-42879600	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr5:42877200-42879800	Enhancers	Brain Anterior Caudate	brain
33	chr5:42877200-42879800	Enhancers	Brain Hippocampus Middle	brain
34	chr5:42877200-42879800	Enhancers	Brain Substantia Nigra	brain
35	chr5:42877400-42878400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr5:42877400-42878800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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