Variant report

Variant	rs1432973
Chromosome Location	chr5:147282545-147282546
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10477355	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11958481	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1432971	0.92[AFR][1000 genomes]
rs1432974	0.83[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs17107413	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17107421	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17703848	0.85[CEU][hapmap]
rs1835968	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1835969	0.90[ASN][1000 genomes]
rs2288781	0.90[AFR][1000 genomes]
rs2304067	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6580506	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580507	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6859879	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862197	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73263247	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7706789	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7722416	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7722926	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021356	chr5:147103627-147310531	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1033907	chr5:147109014-147309076	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv537916	chr5:147109014-147309076	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3334831	chr5:147165950-147339765	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1028477	chr5:147255013-147416217	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1432973	SCGB3A2	cis	multi-tissue	Pritchard

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147273400-147289000	Weak transcription	Left Ventricle	heart
2	chr5:147275600-147283200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:147277400-147284800	Enhancers	NH-A	brain
4	chr5:147279000-147284800	Weak transcription	Osteobl	bone
5	chr5:147279600-147283600	Weak transcription	HMEC	breast
6	chr5:147279800-147285200	Weak transcription	Hela-S3	cervix
7	chr5:147280200-147282600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr5:147280400-147282600	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr5:147280400-147286000	Weak transcription	Stomach Mucosa	stomach
10	chr5:147280600-147282600	Enhancers	Aorta	Aorta
11	chr5:147280600-147283400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:147281400-147283400	Enhancers	Placenta Amnion	Placenta Amnion
13	chr5:147281400-147285800	Weak transcription	HSMMtube	muscle
14	chr5:147281600-147283400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:147281800-147285000	Weak transcription	Fetal Heart	heart
16	chr5:147281800-147285800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:147282400-147283400	Enhancers	Pancreatic Islets	Pancreatic Islet

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links