Variant report

Variant	rs55900888
Chromosome Location	chr2:231293680-231293681
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:231292538..231294481-chr2:231296782..231298607,2	MCF-7	breast:
2	chr2:231292379..231294379-chr2:231300867..231302513,2	K562	blood:

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10202501	0.81[AFR][1000 genomes]
rs12694867	0.81[AFR][1000 genomes]
rs13006418	0.84[AFR][1000 genomes]
rs17273810	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55798834	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62193380	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62193412	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73000209	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73000227	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv584672	chr2:231289976-231348888	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231281600-231294800	Weak transcription	Gastric	stomach
2	chr2:231282000-231294000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:231283600-231293800	Weak transcription	Fetal Lung	lung
4	chr2:231283600-231294800	Weak transcription	HSMM	muscle
5	chr2:231283600-231309200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:231283800-231294600	Weak transcription	Fetal Heart	heart
7	chr2:231283800-231294800	Weak transcription	Esophagus	oesophagus
8	chr2:231284200-231294800	Weak transcription	Lung	lung
9	chr2:231284200-231294800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:231284200-231294800	Weak transcription	Thymus	Thymus
11	chr2:231284200-231301000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:231284200-231304000	Weak transcription	NH-A	brain
13	chr2:231284600-231306200	Weak transcription	HMEC	breast
14	chr2:231288800-231293800	Weak transcription	NHDF-Ad	bronchial
15	chr2:231288800-231319000	Weak transcription	Fetal Kidney	kidney
16	chr2:231288800-231356000	Weak transcription	Stomach Mucosa	stomach
17	chr2:231289000-231293800	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:231289000-231293800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:231289000-231293800	Weak transcription	Osteobl	bone
20	chr2:231289000-231294000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:231289000-231294800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:231289000-231295000	Weak transcription	Right Ventricle	heart
23	chr2:231289000-231299400	Weak transcription	NHLF	lung
24	chr2:231289000-231309200	Weak transcription	Aorta	Aorta
25	chr2:231289200-231293800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:231289200-231294800	Weak transcription	Adipose Nuclei	Adipose
27	chr2:231289200-231294800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr2:231289600-231294800	Weak transcription	Ovary	ovary
29	chr2:231289600-231294800	Weak transcription	Pancreas	Pancrea
30	chr2:231289600-231295400	Weak transcription	Small Intestine	intestine
31	chr2:231290000-231295200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:231290800-231294800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr2:231291000-231295200	ZNF genes & repeats	GM12878-XiMat	blood
34	chr2:231291200-231299600	Weak transcription	NHEK	skin
35	chr2:231291600-231293800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:231291600-231295000	Weak transcription	Hela-S3	cervix
37	chr2:231291800-231293800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:231291800-231294800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr2:231291800-231294800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:231292000-231293800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr2:231292000-231294400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr2:231292000-231294800	Strong transcription	Primary T cells from cord blood	blood
43	chr2:231292200-231293800	Strong transcription	Primary B cells from cord blood	blood
44	chr2:231292200-231294600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:231292200-231294800	Strong transcription	Fetal Thymus	thymus
46	chr2:231292200-231295400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:231292400-231293800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr2:231292400-231293800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr2:231292400-231294600	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr2:231292400-231294800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links