Variant report

Variant	rs55663622
Chromosome Location	chr2:189391763-189391764
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:189389338..189392140-chr2:189468251..189470739,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10153688	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10153871	0.88[EUR][1000 genomes]
rs10172178	0.85[EUR][1000 genomes]
rs10185750	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10203054	0.85[EUR][1000 genomes]
rs10804021	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10931363	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685238	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11695316	0.85[EUR][1000 genomes]
rs11902664	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12475894	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12476413	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12997039	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13025659	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13386581	0.88[EUR][1000 genomes]
rs13386959	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392850	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13393057	0.85[EUR][1000 genomes]
rs13396968	0.89[EUR][1000 genomes]
rs13397653	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13412448	0.88[EUR][1000 genomes]
rs13413644	0.85[EUR][1000 genomes]
rs13414327	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13418031	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13424809	0.85[EUR][1000 genomes]
rs1507551	0.85[EUR][1000 genomes]
rs1807235	0.85[EUR][1000 genomes]
rs4453658	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4577225	0.85[EUR][1000 genomes]
rs4667231	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61045757	0.85[EUR][1000 genomes]
rs6414119	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434285	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434286	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66641143	0.89[EUR][1000 genomes]
rs6707212	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6709557	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6722940	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6727633	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67425558	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6744275	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756504	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7419798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7420808	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7422739	1.00[ASN][1000 genomes]
rs7423554	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7424421	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7568147	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7582643	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7587596	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7600043	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7602180	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584055	chr2:189266823-189493686	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv834489	chr2:189329027-189494224	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1003974	chr2:189331760-189827814	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv533110	chr2:189354436-189462552	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189329200-189399000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:189361800-189392000	Weak transcription	Ovary	ovary
3	chr2:189371800-189394000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:189381000-189394200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:189382400-189393600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:189382400-189394000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:189382800-189394800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:189383200-189422000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:189383200-189423800	Weak transcription	Placenta	Placenta
10	chr2:189384800-189391800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:189384800-189395000	Weak transcription	Gastric	stomach
12	chr2:189384800-189442200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:189385400-189396400	Weak transcription	Psoas Muscle	Psoas
14	chr2:189387800-189404000	Weak transcription	A549	lung
15	chr2:189388000-189393000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:189388200-189391800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:189388200-189434000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr2:189388800-189394200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:189390400-189391800	Enhancers	Colon Smooth Muscle	Colon
20	chr2:189390400-189392000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:189390400-189392000	Enhancers	NHDF-Ad	bronchial
22	chr2:189390400-189392200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:189390400-189392200	Enhancers	Fetal Stomach	stomach
24	chr2:189391000-189392600	Enhancers	HUVEC	blood vessel
25	chr2:189391000-189393000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:189391200-189392200	Enhancers	Osteobl	bone
27	chr2:189391200-189392600	Enhancers	NHLF	lung
28	chr2:189391200-189392800	Enhancers	Fetal Lung	lung
29	chr2:189391400-189392200	Enhancers	Muscle Satellite Cultured Cells	--
30	chr2:189391400-189392200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:189391400-189392600	Enhancers	Brain Germinal Matrix	brain
32	chr2:189391600-189391800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:189391600-189392000	Enhancers	Adipose Nuclei	Adipose
34	chr2:189391600-189392000	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr2:189391600-189392000	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr2:189391600-189392000	Enhancers	NH-A	brain
37	chr2:189391600-189392200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:189391600-189392200	Enhancers	Fetal Heart	heart
39	chr2:189391600-189392200	Flanking Active TSS	Rectal Smooth Muscle	rectum
40	chr2:189391600-189392600	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr2:189391600-189392800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:189391600-189392800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:189391600-189392800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links