Variant report

Variant	rs12496925
Chromosome Location	chr3:111470108-111470109
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10212300	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10470303	0.92[ASN][1000 genomes]
rs10934106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934107	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11710738	0.96[ASN][1000 genomes]
rs12490166	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12490595	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497012	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13069980	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13074817	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13079085	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4284954	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4431081	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4682057	0.99[ASN][1000 genomes]
rs4682305	0.96[ASN][1000 genomes]
rs55938712	0.80[ASN][1000 genomes]
rs62273780	0.96[ASN][1000 genomes]
rs6438003	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6438008	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6438009	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6764720	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6768713	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6777540	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6784753	0.99[ASN][1000 genomes]
rs6786386	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6786612	0.94[ASN][1000 genomes]
rs6790072	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6790079	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6792493	0.86[ASN][1000 genomes]
rs6802995	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7427201	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7609653	1.00[ASN][1000 genomes]
rs7614443	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9818574	0.92[ASN][1000 genomes]
rs9823974	0.91[ASN][1000 genomes]
rs9825915	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9834030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838371	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9863403	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9868171	0.96[ASN][1000 genomes]
rs9870823	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111465400-111470400	Weak transcription	Hela-S3	cervix
2	chr3:111466200-111471400	Enhancers	NHEK	skin
3	chr3:111466400-111471200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:111466400-111471400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:111466600-111471000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:111466800-111471200	Enhancers	HSMM	muscle
7	chr3:111467200-111470600	Weak transcription	Small Intestine	intestine
8	chr3:111467400-111470200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:111467400-111470600	Weak transcription	NH-A	brain
10	chr3:111467400-111470800	Weak transcription	Stomach Mucosa	stomach
11	chr3:111467800-111471400	Enhancers	Muscle Satellite Cultured Cells	--
12	chr3:111468000-111471200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr3:111468000-111471400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr3:111468000-111471400	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr3:111468200-111471200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:111468200-111471200	Enhancers	Osteobl	bone
17	chr3:111468200-111471400	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr3:111468400-111471000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:111468400-111471200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:111468400-111471200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:111468400-111471200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:111468400-111471200	Enhancers	HMEC	breast
23	chr3:111468400-111471400	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr3:111468600-111471000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:111468800-111470400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:111468800-111470800	Weak transcription	Fetal Lung	lung
27	chr3:111469000-111470200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr3:111469000-111470200	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:111469000-111470200	Weak transcription	Fetal Kidney	kidney
30	chr3:111469000-111470800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:111469000-111471000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:111469200-111471000	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr3:111469400-111470200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr3:111469400-111470200	Enhancers	Fetal Muscle Leg	muscle
35	chr3:111469400-111470200	Weak transcription	NHLF	lung
36	chr3:111469400-111470400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:111469400-111471200	Enhancers	H1 Cell Line	embryonic stem cell
38	chr3:111469400-111471200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:111469600-111470200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:111469600-111470200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr3:111469600-111470200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr3:111469600-111470200	Enhancers	Fetal Muscle Trunk	muscle
43	chr3:111469600-111470800	Weak transcription	Fetal Stomach	stomach
44	chr3:111469600-111471000	Enhancers	A549	lung
45	chr3:111469600-111471000	Weak transcription	HSMMtube	muscle
46	chr3:111469600-111471200	Enhancers	Adipose Nuclei	Adipose
47	chr3:111469600-111477800	Weak transcription	Liver	Liver
48	chr3:111469800-111470200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:111470000-111470200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:111470000-111470200	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links