Variant report

Variant	rs55990380
Chromosome Location	chr1:62267821-62267822
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62263282..62264953-chr1:62267149..62270089,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1977737	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55870274	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57065597	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57248449	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72929610	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72929622	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72929633	0.83[AFR][1000 genomes]
rs72929646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72929655	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][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	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3693319	chr1:62207254-62402549	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv830004	chr1:62242944-62382228	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62220200-62290200	Weak transcription	Lung	lung
2	chr1:62220200-62310800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:62222000-62293000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:62224000-62290800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:62225000-62284400	Weak transcription	Psoas Muscle	Psoas
6	chr1:62227800-62294600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:62228600-62391800	Weak transcription	Small Intestine	intestine
8	chr1:62231800-62273400	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:62233400-62288800	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:62235400-62288800	Weak transcription	A549	lung
11	chr1:62242200-62274400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr1:62243000-62270600	Weak transcription	Spleen	Spleen
13	chr1:62247600-62287400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr1:62247600-62297400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:62250000-62302800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:62251200-62268400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:62251200-62288600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:62251200-62306400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr1:62251800-62272600	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:62252000-62275800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:62253000-62274400	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:62253600-62297400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:62253800-62271200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:62253800-62289000	Weak transcription	HepG2	liver
25	chr1:62254000-62286400	Weak transcription	Aorta	Aorta
26	chr1:62254000-62288600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr1:62254200-62288400	Weak transcription	Adipose Nuclei	Adipose
28	chr1:62255600-62302400	Weak transcription	Brain Anterior Caudate	brain
29	chr1:62257000-62291600	Weak transcription	Gastric	stomach
30	chr1:62258400-62268800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:62260000-62275600	Weak transcription	Fetal Heart	heart
32	chr1:62260800-62272000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:62262800-62273400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:62263000-62268800	Strong transcription	Liver	Liver
35	chr1:62263400-62280800	Weak transcription	Esophagus	oesophagus
36	chr1:62263400-62293200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr1:62263600-62288400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:62263800-62303800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr1:62263800-62343600	Weak transcription	Colonic Mucosa	Colon
40	chr1:62264200-62268400	Weak transcription	NHEK	skin
41	chr1:62264200-62290200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr1:62264600-62271200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:62264600-62273200	Weak transcription	Fetal Intestine Large	intestine
44	chr1:62264600-62283800	Weak transcription	Primary T cells from cord blood	blood
45	chr1:62264600-62286400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:62264600-62286400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr1:62264600-62287800	Weak transcription	Left Ventricle	heart
48	chr1:62264600-62292800	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr1:62264600-62296000	Weak transcription	Fetal Brain Female	brain
50	chr1:62264600-62297400	Weak transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links