Variant report

Variant	rs331139
Chromosome Location	chr3:78926499-78926500
allele	C/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:38)

rs_ID	r²[population]
rs162262	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs162263	0.82[EUR][1000 genomes]
rs162425	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs162426	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs162427	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs162428	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs162429	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs186648	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs329805	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs329811	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs329812	0.87[EUR][1000 genomes]
rs329816	0.82[EUR][1000 genomes]
rs329818	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs329819	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs329820	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs329821	0.84[ASN][1000 genomes]
rs329822	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs329824	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs331143	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331145	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs331149	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs331161	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs331162	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs331163	0.89[EUR][1000 genomes]
rs331164	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs331181	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs331182	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs331184	0.80[EUR][1000 genomes]
rs331188	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs331189	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs331190	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs331199	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs379346	0.81[ASN][1000 genomes]
rs388421	0.80[ASN][1000 genomes]
rs432141	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs484531	0.80[ASN][1000 genomes]
rs531125	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6800782	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv834744	chr3:78911545-79076470	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv877020	chr3:78913203-78975982	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv470672	chr3:78913203-78985805	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv590734	chr3:78915205-78985805	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv590735	chr3:78922852-78977507	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78917400-78927000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr3:78918000-78928800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:78918000-78929800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:78918800-78927400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:78920400-78927000	Weak transcription	Aorta	Aorta
6	chr3:78920800-78927000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:78921600-78927000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:78921600-78936000	Weak transcription	HSMM	muscle
9	chr3:78921600-78936600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:78921800-78927000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:78921800-78928400	Weak transcription	Brain Germinal Matrix	brain
12	chr3:78921800-78928600	Weak transcription	Fetal Lung	lung
13	chr3:78922000-78927000	Weak transcription	NH-A	brain
14	chr3:78922000-78929800	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:78922200-78926800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:78922600-78928600	Weak transcription	Brain Angular Gyrus	brain
17	chr3:78922600-78944000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:78923000-78943800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:78923200-78926600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:78923200-78928400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:78925000-78926800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:78925000-78928800	Weak transcription	Adipose Nuclei	Adipose
23	chr3:78925000-78930800	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr3:78925200-78926600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:78925200-78927000	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:78925200-78927000	Weak transcription	NHLF	lung
27	chr3:78925200-78928600	Weak transcription	Fetal Brain Female	brain
28	chr3:78925200-78929600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:78925200-78929800	Weak transcription	Brain Anterior Caudate	brain
30	chr3:78925400-78927000	Weak transcription	HepG2	liver
31	chr3:78925400-78927000	Weak transcription	NHDF-Ad	bronchial
32	chr3:78925400-78927200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:78925400-78927200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:78925400-78927400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:78925400-78928400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:78925400-78929400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:78925800-78927000	Weak transcription	Osteobl	bone
38	chr3:78926000-78927400	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr3:78926000-78927600	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr3:78926000-78927600	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr3:78926200-78926600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr3:78926200-78928200	Weak transcription	Brain Substantia Nigra	brain
43	chr3:78926200-78928800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:78926400-78926800	Weak transcription	Brain Cingulate Gyrus	brain

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