Variant report

Variant	rs55869062
Chromosome Location	chr5:177068387-177068388
allele	C/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:23)

rs_ID	r²[population]
rs28499092	0.84[EUR][1000 genomes]
rs28595585	0.97[EUR][1000 genomes]
rs55646352	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55975666	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56190755	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56664111	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57593509	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57960711	0.94[EUR][1000 genomes]
rs59621415	0.94[EUR][1000 genomes]
rs59666704	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60634107	0.94[EUR][1000 genomes]
rs61334447	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73337744	0.94[EUR][1000 genomes]
rs73337753	0.94[EUR][1000 genomes]
rs73337757	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73337765	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73337767	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73337782	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73337783	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73337790	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73339755	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73339759	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs901380	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916108	chr5:176688459-177078723	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
2	nsv1024444	chr5:176751921-177427715	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	142 gene(s)	inside rSNPs	diseases
3	esv2752795	chr5:176898619-177488281	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	nsv883182	chr5:176980995-177322056	Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv969021	chr5:177060702-177111251	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3388835	chr5:177066446-177068444	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177046600-177068400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:177046600-177069200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:177046600-177069600	Weak transcription	Esophagus	oesophagus
4	chr5:177046800-177084000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr5:177047000-177079000	Weak transcription	Colon Smooth Muscle	Colon
6	chr5:177047200-177070800	Weak transcription	Pancreas	Pancrea
7	chr5:177047400-177075000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:177047800-177069000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:177047800-177080200	Weak transcription	Primary B cells from cord blood	blood
10	chr5:177048000-177069000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr5:177048800-177083600	Weak transcription	Fetal Lung	lung
12	chr5:177051600-177069000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:177051800-177080200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr5:177052000-177083200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr5:177052000-177085600	Weak transcription	Gastric	stomach
16	chr5:177052200-177070000	Weak transcription	Primary T cells from cord blood	blood
17	chr5:177052800-177070200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr5:177052800-177070200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr5:177052800-177070400	Weak transcription	Adipose Nuclei	Adipose
20	chr5:177052800-177076400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr5:177054000-177084600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr5:177054200-177069200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr5:177054200-177070000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr5:177054400-177096000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr5:177059000-177068400	Weak transcription	Aorta	Aorta
26	chr5:177066600-177069000	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr5:177066800-177083000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:177067000-177070000	Weak transcription	Fetal Brain Female	brain
29	chr5:177067000-177071200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:177067000-177073800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:177067000-177075000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:177067000-177084000	Weak transcription	Dnd41	blood
33	chr5:177067200-177075000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr5:177067200-177075000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr5:177067200-177083200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:177067800-177068400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr5:177068000-177068800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:177068200-177068400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr5:177068200-177068400	Strong transcription	Lung	lung
40	chr5:177068200-177068400	Active TSS	Spleen	Spleen
41	chr5:177068200-177068600	ZNF genes & repeats	Fetal Intestine Large	intestine
42	chr5:177068200-177068800	Strong transcription	Ovary	ovary
43	chr5:177068200-177068800	Strong transcription	Monocytes-CD14+_RO01746	blood

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