Variant report

Variant	rs1421938
Chromosome Location	chr5:52338806-52338807
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10051913	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10068849	0.88[AFR][1000 genomes]
rs11955860	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12520747	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1421933	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1421934	0.81[ASN][1000 genomes]
rs1549276	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2056403	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2112290	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2216729	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2406598	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3212434	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3212452	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212469	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3212476	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3212530	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3797499	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7719848	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7731858	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7736005	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs988557	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs988558	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs988559	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv880425	chr5:52291279-52345868	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv881652	chr5:52323568-52385312	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv880389	chr5:52333420-52375199	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv881217	chr5:52334774-52341512	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv881071	chr5:52334774-52362765	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52314200-52348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:52324400-52356400	Weak transcription	Brain Anterior Caudate	brain
3	chr5:52327800-52344200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:52328000-52369200	Weak transcription	Fetal Intestine Small	intestine
5	chr5:52328800-52348000	Weak transcription	Fetal Intestine Large	intestine
6	chr5:52333400-52341400	Strong transcription	HepG2	liver
7	chr5:52333800-52348800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:52333800-52369800	Weak transcription	Colonic Mucosa	Colon
9	chr5:52333800-52392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr5:52334000-52360800	Weak transcription	Small Intestine	intestine
11	chr5:52334400-52348000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:52334600-52343400	Weak transcription	Gastric	stomach
13	chr5:52334600-52348400	Weak transcription	Lung	lung
14	chr5:52334800-52343400	Weak transcription	Esophagus	oesophagus
15	chr5:52334800-52343800	Weak transcription	Brain Hippocampus Middle	brain
16	chr5:52334800-52343800	Weak transcription	Pancreas	Pancrea
17	chr5:52334800-52348000	Weak transcription	Brain Substantia Nigra	brain
18	chr5:52334800-52380800	Weak transcription	Stomach Mucosa	stomach
19	chr5:52334800-52391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:52337000-52340800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:52337200-52353400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr5:52337400-52339000	Strong transcription	NHEK	skin
24	chr5:52337400-52340200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:52337400-52340600	Weak transcription	Hela-S3	cervix
26	chr5:52337400-52340600	Weak transcription	Osteobl	bone
27	chr5:52337400-52340800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr5:52337400-52346400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr5:52337400-52348800	Weak transcription	A549	lung
30	chr5:52337400-52355200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr5:52337400-52369000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr5:52337400-52370200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:52337600-52340600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:52337600-52340800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:52337600-52340800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr5:52337600-52340800	Weak transcription	NHDF-Ad	bronchial
37	chr5:52337800-52340600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:52337800-52340600	Weak transcription	NH-A	brain
39	chr5:52337800-52341800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:52337800-52343200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:52338000-52339400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr5:52338000-52348200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr5:52338400-52339400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr5:52338400-52341000	Weak transcription	Dnd41	blood
45	chr5:52338600-52340600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:52338800-52339200	Weak transcription	HUVEC	blood vessel
47	chr5:52338800-52340200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr5:52338800-52340200	Weak transcription	HMEC	breast
49	chr5:52338800-52340600	Weak transcription	NHLF	lung

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