Variant report

Variant	rs55798475
Chromosome Location	chr5:112209134-112209135
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs17135067	0.93[EUR][1000 genomes]
rs17135193	0.86[EUR][1000 genomes]
rs17285666	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17285827	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17286230	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17290064	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17310536	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17311019	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17311096	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17359859	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17360045	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17360289	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17369211	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17369487	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17370550	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17371015	0.93[EUR][1000 genomes]
rs1833560	0.86[EUR][1000 genomes]
rs4519915	1.00[AMR][1000 genomes]
rs55684649	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55771309	0.81[EUR][1000 genomes]
rs55771959	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55901036	1.00[AMR][1000 genomes]
rs55940904	1.00[AMR][1000 genomes]
rs56023848	1.00[AMR][1000 genomes]
rs56052440	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56155803	0.81[EUR][1000 genomes]
rs56194248	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56218335	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56235416	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56265422	1.00[AMR][1000 genomes]
rs56320268	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56321569	0.93[EUR][1000 genomes]
rs56328836	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56405915	0.81[EUR][1000 genomes]
rs57043077	0.93[EUR][1000 genomes]
rs60532731	0.81[EUR][1000 genomes]
rs6594657	1.00[AMR][1000 genomes]
rs6594658	1.00[AMR][1000 genomes]
rs6862944	1.00[AMR][1000 genomes]
rs6881198	0.89[AMR][1000 genomes]
rs6881233	1.00[AMR][1000 genomes]
rs6881426	0.89[AMR][1000 genomes]
rs73216225	0.93[EUR][1000 genomes]
rs73220038	0.93[EUR][1000 genomes]
rs73220063	0.86[EUR][1000 genomes]
rs7704566	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7728495	1.00[AMR][1000 genomes]
rs7728766	0.93[EUR][1000 genomes]
rs7730441	0.86[EUR][1000 genomes]
rs7730944	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs878074	1.00[AMR][1000 genomes]
rs878075	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv529536	chr5:112174106-112269758	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv870231	chr5:112192379-112247084	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1029595	chr5:112197662-112242375	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1030103	chr5:112197662-112255712	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv537863	chr5:112197662-112255712	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv4960	chr5:112200199-112218299	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112197800-112211800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:112198400-112211200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:112198400-112220600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:112199000-112226000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:112199200-112210200	Weak transcription	Psoas Muscle	Psoas
6	chr5:112199200-112213200	Weak transcription	Fetal Heart	heart
7	chr5:112199200-112213400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:112199400-112215000	Weak transcription	Small Intestine	intestine
9	chr5:112199600-112214400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr5:112199800-112212200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr5:112200600-112213800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr5:112200600-112242000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:112201000-112209400	Strong transcription	Osteobl	bone
14	chr5:112202800-112217800	Weak transcription	Brain Substantia Nigra	brain
15	chr5:112203400-112213000	Weak transcription	Fetal Lung	lung
16	chr5:112203400-112218200	Weak transcription	Colonic Mucosa	Colon
17	chr5:112203600-112214400	Weak transcription	Stomach Mucosa	stomach
18	chr5:112203800-112211000	Weak transcription	HepG2	liver
19	chr5:112204000-112212000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:112204000-112213800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr5:112205000-112214600	Weak transcription	Fetal Kidney	kidney
22	chr5:112205200-112212800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr5:112205400-112213600	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr5:112205600-112212800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr5:112206200-112209400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr5:112206200-112218400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:112206400-112209400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr5:112206400-112210600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr5:112206400-112211600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr5:112206400-112212200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:112206400-112213800	Weak transcription	HUVEC	blood vessel
32	chr5:112206400-112242800	Weak transcription	Fetal Brain Male	brain
33	chr5:112206600-112209600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr5:112206600-112209800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr5:112206600-112209800	Weak transcription	HSMM	muscle
36	chr5:112206600-112209800	Weak transcription	NH-A	brain
37	chr5:112206600-112210000	Weak transcription	Primary B cells from cord blood	blood
38	chr5:112206600-112210600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr5:112206600-112211200	Weak transcription	K562	blood
40	chr5:112206600-112211800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr5:112206600-112213000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr5:112206600-112213200	Weak transcription	Brain Germinal Matrix	brain
43	chr5:112206600-112213200	Weak transcription	Fetal Brain Female	brain
44	chr5:112206600-112213400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr5:112206600-112214000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr5:112206600-112214200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr5:112206600-112214400	Weak transcription	Hela-S3	cervix
48	chr5:112206600-112215400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr5:112206600-112215800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr5:112206600-112216400	Weak transcription	Aorta	Aorta

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