Variant report

Variant	rs2699880
Chromosome Location	chr3:133115340-133115341
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	chr3:133110660..133112809-chr3:133115300..133117323,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1114630	0.83[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1153876	0.84[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1197287	0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1197288	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1197289	0.82[CHB][hapmap]
rs1197296	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1197297	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1197298	0.88[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1197299	0.82[ASW][hapmap];0.88[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1197301	0.97[ASN][1000 genomes]
rs1197302	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1197304	0.83[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1197305	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1197306	0.88[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1197309	0.87[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1197313	0.83[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1197314	0.83[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1201671	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1201673	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12631678	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1619552	0.87[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1619622	0.87[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1708376	0.89[ASN][1000 genomes]
rs1708377	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1708384	0.88[ASN][1000 genomes]
rs1708385	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1795104	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1795107	0.87[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2089987	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2670179	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2699882	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3732572	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4854583	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4854719	0.83[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4854720	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56181416	0.81[ASN][1000 genomes]
rs656721	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs6780144	0.82[ASN][1000 genomes]
rs6802663	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs869751	0.82[CHB][hapmap]
rs938230	0.82[CHB][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.80[ASN][1000 genomes]
rs9850193	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9853752	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9853757	0.89[EUR][1000 genomes];0.88[ASN][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	nsv460857	chr3:133101390-133122216	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv591801	chr3:133101390-133122216	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133099000-133117000	Weak transcription	Placenta	Placenta
2	chr3:133099600-133122600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:133103400-133123200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:133103400-133123600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:133103800-133115800	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:133103800-133118600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:133103800-133123800	Weak transcription	Brain Anterior Caudate	brain
8	chr3:133104000-133122200	Weak transcription	Brain Substantia Nigra	brain
9	chr3:133104400-133131400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:133107200-133123800	Weak transcription	Fetal Thymus	thymus
11	chr3:133110000-133120400	Weak transcription	Brain Angular Gyrus	brain
12	chr3:133110200-133120400	Weak transcription	Fetal Brain Male	brain
13	chr3:133110800-133123600	Weak transcription	HSMM	muscle
14	chr3:133112600-133119400	Strong transcription	Fetal Brain Female	brain
15	chr3:133112600-133120400	Weak transcription	Brain Hippocampus Middle	brain
16	chr3:133112600-133122200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:133113000-133116000	Weak transcription	Left Ventricle	heart
18	chr3:133113200-133117000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:133113200-133118600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:133113400-133116200	Strong transcription	Brain Germinal Matrix	brain
21	chr3:133113400-133120000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:133113400-133122200	Weak transcription	Fetal Lung	lung
23	chr3:133113600-133123600	Weak transcription	HSMMtube	muscle
24	chr3:133114200-133116200	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:133114200-133117400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:133114200-133127400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:133114800-133120200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:133115200-133115800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:133115200-133116000	Strong transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links