Variant report

Variant	rs296406
Chromosome Location	chr5:58893018-58893019
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10059809	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10065078	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1395335	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1395336	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs1395337	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs294481	0.82[JPT][hapmap]
rs294494	0.86[CEU][hapmap]
rs294496	0.86[CEU][hapmap]
rs294497	0.86[CEU][hapmap]
rs294498	0.86[CEU][hapmap]
rs295946	0.87[CEU][hapmap]
rs295952	0.80[AMR][1000 genomes]
rs295959	0.80[AMR][1000 genomes]
rs295973	0.87[CEU][hapmap]
rs37579	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs40215	0.89[CHB][hapmap]
rs6858964	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs6890180	0.84[ASN][1000 genomes]
rs697076	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs702544	0.88[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58883800-58894200	Weak transcription	Aorta	Aorta
2	chr5:58884200-58893800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:58884200-58894000	Weak transcription	Right Atrium	heart
4	chr5:58884200-58894200	Weak transcription	Liver	Liver
5	chr5:58884200-58902800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:58884600-58893800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:58885000-58894200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:58887000-58894200	Weak transcription	Fetal Intestine Large	intestine
9	chr5:58887000-58894200	Weak transcription	GM12878-XiMat	blood
10	chr5:58887400-58894000	Weak transcription	Brain Substantia Nigra	brain
11	chr5:58888200-58894000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr5:58888200-58894200	Weak transcription	Psoas Muscle	Psoas
13	chr5:58888400-58894000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr5:58888400-58894200	Weak transcription	Colon Smooth Muscle	Colon
15	chr5:58889600-58894200	Weak transcription	Brain Angular Gyrus	brain
16	chr5:58889800-58894200	Weak transcription	Fetal Intestine Small	intestine
17	chr5:58891600-58893800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr5:58892200-58893200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:58892200-58894000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:58892200-58894200	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr5:58892200-58894200	Enhancers	Muscle Satellite Cultured Cells	--
22	chr5:58892200-58894200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:58892200-58894800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:58892400-58893200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:58892400-58894000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:58892400-58894200	Enhancers	NHEK	skin
27	chr5:58892600-58893200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr5:58892600-58893200	Enhancers	Duodenum Mucosa	Duodenum
29	chr5:58892600-58893200	Enhancers	Rectal Smooth Muscle	rectum
30	chr5:58892600-58893200	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr5:58892600-58893200	Enhancers	NH-A	brain
32	chr5:58892600-58893200	Enhancers	Osteobl	bone
33	chr5:58892600-58893400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr5:58892600-58893400	Flanking Active TSS	A549	lung
35	chr5:58892600-58893400	Enhancers	NHDF-Ad	bronchial
36	chr5:58892600-58893600	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr5:58892600-58893600	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr5:58892600-58894000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr5:58892600-58894200	Enhancers	Stomach Mucosa	stomach
40	chr5:58892600-58894200	Enhancers	Hela-S3	cervix
41	chr5:58892600-58894200	Enhancers	HMEC	breast
42	chr5:58892600-58894200	Enhancers	HSMM	muscle
43	chr5:58892600-58894200	Enhancers	HUVEC	blood vessel
44	chr5:58892800-58893800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr5:58892800-58894200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr5:58892800-58894800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:58892800-58894800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:58893000-58893200	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr5:58893000-58893400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr5:58893000-58893400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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