Variant report

Variant	rs333492
Chromosome Location	chr3:78861145-78861146
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12330466	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12330828	0.81[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13319888	1.00[AMR][1000 genomes]
rs162816	1.00[LWK][hapmap];0.92[MKK][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs173004	0.88[LWK][hapmap];0.87[MKK][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs231606	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs333473	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs333480	0.82[AFR][1000 genomes]
rs333482	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs333494	1.00[AMR][1000 genomes]
rs333496	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs333500	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs333504	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs333505	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs333509	1.00[AMR][1000 genomes]
rs333510	0.81[YRI][hapmap]
rs365492	1.00[AMR][1000 genomes]
rs365924	1.00[AMR][1000 genomes]
rs375298	1.00[AMR][1000 genomes]
rs383189	0.94[LWK][hapmap];0.92[MKK][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs390060	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs408455	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs416640	0.93[YRI][hapmap];1.00[AMR][1000 genomes]
rs72892483	1.00[AMR][1000 genomes]
rs72894478	0.91[AFR][1000 genomes]
rs72896415	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9631524	1.00[AMR][1000 genomes]
rs9631525	1.00[AMR][1000 genomes]
rs9810277	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9813851	0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9817612	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9822237	0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9841731	0.86[AFR][1000 genomes]
rs9849099	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9861640	0.83[YRI][hapmap]
rs9872311	0.91[AFR][1000 genomes];1.00[AMR][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	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	nsv877019	chr3:78808850-78877217	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv432459	chr3:78819310-78874310	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78851400-78880400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:78851600-78861200	Weak transcription	Brain Angular Gyrus	brain
3	chr3:78854200-78864000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:78854200-78865400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:78854200-78872600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:78854400-78871200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:78855400-78861400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:78855400-78872600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:78856800-78864000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:78859400-78861600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:78859600-78861800	Enhancers	Fetal Lung	lung
12	chr3:78859600-78863000	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:78860200-78871600	Weak transcription	HepG2	liver
14	chr3:78860600-78861200	Enhancers	Brain Substantia Nigra	brain
15	chr3:78860800-78869600	Weak transcription	Fetal Brain Male	brain
16	chr3:78861000-78861400	Weak transcription	Fetal Stomach	stomach
17	chr3:78861000-78861600	Enhancers	H9 Cell Line	embryonic stem cell
18	chr3:78861000-78861800	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr3:78861000-78861800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr3:78861000-78861800	Enhancers	Fetal Brain Female	brain
21	chr3:78861000-78867600	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:78861000-78872600	Weak transcription	Brain Anterior Caudate	brain

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