Variant report

Variant	rs55689727
Chromosome Location	chr5:52882735-52882736
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10940327	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11749138	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11949787	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11956779	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12514303	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12517465	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12518490	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12522861	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2087618	0.92[ASN][1000 genomes]
rs2124948	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2168662	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2290697	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs269414	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28507151	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35119962	0.88[ASN][1000 genomes]
rs35879821	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147736	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4362905	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4640749	0.84[AFR][1000 genomes]
rs55791118	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56185221	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56402244	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs567	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60308929	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6450151	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6860913	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6897299	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72750137	0.87[ASN][1000 genomes]
rs72751836	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72753643	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7712013	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7737530	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv880868	chr5:52799618-53002783	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv880689	chr5:52847995-53002783	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52857800-52883000	Weak transcription	Hela-S3	cervix
2	chr5:52857800-52884000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:52857800-52892800	Weak transcription	Primary B cells from cord blood	blood
4	chr5:52857800-52898800	Weak transcription	HSMM	muscle
5	chr5:52858000-52899800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr5:52858000-52900400	Weak transcription	Fetal Kidney	kidney
7	chr5:52858200-52885000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr5:52858200-52897200	Weak transcription	NHEK	skin
9	chr5:52858400-52895000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:52858400-52899800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr5:52860000-52909000	Weak transcription	Small Intestine	intestine
12	chr5:52860200-52885600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:52860600-52884800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:52861600-52894600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:52865000-52900400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:52865200-52885200	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr5:52865600-52883400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr5:52865600-52898400	Weak transcription	Fetal Lung	lung
19	chr5:52865600-52899800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr5:52866200-52883400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr5:52866400-52884200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:52867600-52888400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr5:52868200-52885200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:52869600-52896000	Weak transcription	Fetal Stomach	stomach
25	chr5:52870200-52892000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:52872000-52892800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr5:52872200-52885000	Weak transcription	Primary T cells from cord blood	blood
28	chr5:52873000-52884800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr5:52873000-52887000	Weak transcription	Brain Hippocampus Middle	brain
30	chr5:52873000-52889200	Weak transcription	A549	lung
31	chr5:52873000-52900400	Weak transcription	Gastric	stomach
32	chr5:52873200-52899000	Weak transcription	Right Atrium	heart
33	chr5:52873400-52885400	Weak transcription	Left Ventricle	heart
34	chr5:52873400-52889800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr5:52874400-52884000	Weak transcription	Fetal Intestine Small	intestine
36	chr5:52874400-52885200	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr5:52874400-52888400	Weak transcription	Fetal Heart	heart
38	chr5:52874600-52889800	Weak transcription	HepG2	liver
39	chr5:52875000-52885400	Weak transcription	Aorta	Aorta
40	chr5:52875000-52900000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr5:52875400-52899200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr5:52875600-52889400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:52876800-52907400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr5:52877200-52884800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr5:52877400-52885800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr5:52877400-52900400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr5:52877600-52898800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:52878400-52885400	Weak transcription	Psoas Muscle	Psoas
49	chr5:52878400-52899000	Weak transcription	Ovary	ovary
50	chr5:52878400-52901200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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