Variant report

Variant	rs2546212
Chromosome Location	chr5:118844150-118844151
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1143650	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2431545	1.00[AFR][1000 genomes]
rs2546206	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2546207	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2546208	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2546209	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2560719	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2560720	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2560721	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2560722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2560724	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2636960	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2636965	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2636967	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2636970	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2652698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2678068	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2678069	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2678072	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2678073	1.00[AMR][1000 genomes]
rs2678075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2678077	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2678082	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2678083	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2678093	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34053410	1.00[AMR][1000 genomes]
rs35121430	1.00[AMR][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	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1024455	chr5:118770429-119487982	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1016271	chr5:118836891-119487982	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer 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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118791800-118846600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:118794800-118861200	Weak transcription	HSMM	muscle
3	chr5:118804200-118879600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr5:118806000-118846400	Weak transcription	Esophagus	oesophagus
5	chr5:118806000-118846400	Weak transcription	Spleen	Spleen
6	chr5:118806200-118844800	Weak transcription	Thymus	Thymus
7	chr5:118806200-118846400	Weak transcription	Pancreas	Pancrea
8	chr5:118806200-118855600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:118806400-118845000	Weak transcription	Fetal Stomach	stomach
10	chr5:118806400-118846400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:118806800-118845400	Weak transcription	Fetal Heart	heart
12	chr5:118812000-118846400	Weak transcription	NHLF	lung
13	chr5:118814000-118845000	Weak transcription	Gastric	stomach
14	chr5:118814000-118845200	Weak transcription	Aorta	Aorta
15	chr5:118814800-118844800	Weak transcription	Lung	lung
16	chr5:118815800-118845400	Weak transcription	HMEC	breast
17	chr5:118816000-118847000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr5:118817000-118846400	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr5:118819600-118844400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr5:118820200-118846400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr5:118827600-118847800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:118829800-118844800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr5:118830400-118845200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr5:118832400-118878200	Weak transcription	NH-A	brain
25	chr5:118832600-118844400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:118832600-118868600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr5:118832800-118844600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:118833000-118860200	Weak transcription	Stomach Mucosa	stomach
29	chr5:118833200-118845000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr5:118833200-118845000	Weak transcription	Ovary	ovary
31	chr5:118833200-118845000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr5:118833200-118846000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:118834400-118847800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr5:118834800-118846400	Weak transcription	Small Intestine	intestine
35	chr5:118836000-118844800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:118836000-118844800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr5:118836000-118850600	Weak transcription	HUVEC	blood vessel
38	chr5:118836600-118846400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr5:118837600-118846200	Weak transcription	HepG2	liver
40	chr5:118837800-118844400	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr5:118837800-118844400	Weak transcription	Left Ventricle	heart
42	chr5:118838000-118869200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr5:118839800-118844400	Weak transcription	Right Ventricle	heart
44	chr5:118839800-118844800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr5:118840000-118844400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr5:118840000-118844400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr5:118840000-118845000	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr5:118840000-118845200	Weak transcription	Colon Smooth Muscle	Colon
49	chr5:118840000-118845400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr5:118840000-118846000	Weak transcription	Fetal Thymus	thymus

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