Variant report

Variant	rs58478669
Chromosome Location	chr3:56816245-56816246
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10510788	0.89[AMR][1000 genomes]
rs11130547	0.87[AMR][1000 genomes]
rs12054242	0.87[AMR][1000 genomes]
rs17288908	0.89[AMR][1000 genomes]
rs2317250	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2317251	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35550387	0.85[AMR][1000 genomes]
rs55837354	0.85[AMR][1000 genomes]
rs55993130	0.88[AMR][1000 genomes]
rs56122263	0.89[AMR][1000 genomes]
rs56134339	0.85[AMR][1000 genomes]
rs56201611	0.85[AMR][1000 genomes]
rs57620263	0.89[AMR][1000 genomes]
rs60374893	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60882397	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62252679	0.87[AMR][1000 genomes]
rs6795927	0.86[AMR][1000 genomes]
rs7611544	0.85[AMR][1000 genomes]
rs7625636	0.86[AMR][1000 genomes]
rs984796	0.87[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876818	chr3:56805376-56924711	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56793200-56817400	Weak transcription	Hela-S3	cervix
2	chr3:56796800-56816400	Weak transcription	Colonic Mucosa	Colon
3	chr3:56805800-56816800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:56806400-56816800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr3:56806400-56817000	Weak transcription	NHEK	skin
6	chr3:56807000-56833200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:56807600-56818000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:56807800-56817400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:56808200-56816800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:56808600-56816800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr3:56809000-56816800	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr3:56810000-56816600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr3:56810000-56822200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:56810200-56817000	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr3:56810400-56816400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr3:56810400-56816400	Weak transcription	Fetal Muscle Leg	muscle
17	chr3:56810400-56817000	Weak transcription	Right Ventricle	heart
18	chr3:56810400-56817000	Weak transcription	Spleen	Spleen
19	chr3:56810400-56818000	Weak transcription	Placenta	Placenta
20	chr3:56810400-56819000	Weak transcription	Fetal Brain Female	brain
21	chr3:56810800-56816400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:56811000-56816400	Weak transcription	Brain Anterior Caudate	brain
23	chr3:56811000-56816400	Weak transcription	Fetal Lung	lung
24	chr3:56811600-56817000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr3:56811800-56816400	Genic enhancers	Dnd41	blood
26	chr3:56812000-56816400	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr3:56812000-56816400	Weak transcription	Brain Substantia Nigra	brain
28	chr3:56812000-56817000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:56812000-56817800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:56812200-56816400	Weak transcription	Adipose Nuclei	Adipose
31	chr3:56812400-56818200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:56812400-56818600	Weak transcription	Brain Angular Gyrus	brain
33	chr3:56813600-56816400	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr3:56813600-56816800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr3:56814000-56816800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr3:56814000-56817600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:56814600-56826800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:56814800-56816800	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr3:56814800-56826600	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr3:56815000-56816400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:56815000-56816800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:56815000-56817400	Enhancers	Thymus	Thymus
43	chr3:56815200-56816800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:56815200-56816800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr3:56815400-56820200	Enhancers	Psoas Muscle	Psoas
46	chr3:56815600-56817000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:56815600-56818200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr3:56815600-56820000	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr3:56815600-56820800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:56815600-56823400	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links