Variant report

Variant	rs11747378
Chromosome Location	chr5:59094755-59094756
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10514856	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs10514881	0.87[AMR][1000 genomes]
rs10940647	0.89[EUR][1000 genomes]
rs10940648	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs11738448	0.83[CEU][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11741470	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs13164391	0.82[EUR][1000 genomes]
rs13168643	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13177163	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs13186779	0.82[EUR][1000 genomes]
rs1504985	0.83[CEU][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2938781	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2938782	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2938787	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2963820	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2963823	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs298056	0.82[CEU][hapmap]
rs298069	0.81[CEU][hapmap]
rs298087	0.83[EUR][1000 genomes]
rs3111174	0.81[CEU][hapmap];0.89[AMR][1000 genomes]
rs35302677	0.82[EUR][1000 genomes]
rs35339176	0.82[EUR][1000 genomes]
rs35526661	0.87[EUR][1000 genomes]
rs59251157	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62370530	0.84[EUR][1000 genomes]
rs877744	0.94[CEU][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59086000-59094800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr5:59086600-59095400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr5:59086800-59095200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:59086800-59095400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:59087400-59095800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr5:59087400-59106000	Weak transcription	Aorta	Aorta
7	chr5:59089800-59095600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr5:59090000-59094800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:59090000-59094800	Weak transcription	HSMM	muscle
10	chr5:59090000-59094800	Weak transcription	NH-A	brain
11	chr5:59090000-59094800	Weak transcription	NHDF-Ad	bronchial
12	chr5:59090000-59095400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr5:59090000-59095800	Weak transcription	Brain Substantia Nigra	brain
14	chr5:59090200-59094800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr5:59090200-59095200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr5:59090400-59095000	Weak transcription	Fetal Brain Female	brain
17	chr5:59090600-59095600	Weak transcription	Brain Anterior Caudate	brain
18	chr5:59091400-59096400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:59092400-59095200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr5:59092400-59095600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr5:59093200-59096000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr5:59093800-59096200	Enhancers	Primary B cells from peripheral blood	blood
23	chr5:59094000-59095000	Enhancers	Colon Smooth Muscle	Colon
24	chr5:59094000-59096400	Enhancers	Fetal Brain Male	brain
25	chr5:59094200-59094800	Enhancers	HUVEC	blood vessel
26	chr5:59094200-59096600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:59094400-59094800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:59094400-59094800	Enhancers	Duodenum Mucosa	Duodenum
29	chr5:59094400-59094800	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr5:59094400-59094800	Flanking Active TSS	A549	lung
31	chr5:59094400-59094800	Enhancers	GM12878-XiMat	blood
32	chr5:59094400-59095000	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr5:59094400-59095000	Enhancers	Adipose Nuclei	Adipose
34	chr5:59094400-59096000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr5:59094400-59096000	Enhancers	Fetal Kidney	kidney
36	chr5:59094400-59096000	Flanking Active TSS	Hela-S3	cervix
37	chr5:59094400-59096600	Enhancers	HMEC	breast
38	chr5:59094600-59094800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr5:59094600-59094800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:59094600-59094800	Enhancers	Muscle Satellite Cultured Cells	--
41	chr5:59094600-59094800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:59094600-59094800	Enhancers	Psoas Muscle	Psoas
43	chr5:59094600-59094800	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr5:59094600-59094800	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr5:59094600-59094800	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr5:59094600-59094800	Enhancers	Stomach Smooth Muscle	stomach
47	chr5:59094600-59095000	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr5:59094600-59095000	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr5:59094600-59095000	Enhancers	Fetal Muscle Leg	muscle
50	chr5:59094600-59095000	Flanking Active TSS	Rectal Smooth Muscle	rectum

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