Variant report

Variant	rs1780746
Chromosome Location	chr1:79182561-79182562
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1033999	0.88[MEX][hapmap]
rs10873993	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11162527	1.00[ASN][1000 genomes]
rs11162543	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1571152	0.83[CHD][hapmap];0.88[MEX][hapmap]
rs1628313	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17394028	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1780743	0.83[CHD][hapmap];0.88[MEX][hapmap]

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	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv830315	chr1:79008443-79200591	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv491784	chr1:79146141-79853482	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv871588	chr1:79164901-79214489	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1780746	ST6GALNAC3	cis	parietal	SCAN
rs1780746	TYW3	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79178400-79184800	Enhancers	Muscle Satellite Cultured Cells	--
2	chr1:79178400-79185000	Enhancers	Osteobl	bone
3	chr1:79179800-79183400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:79180000-79184600	Enhancers	NHDF-Ad	bronchial
5	chr1:79180600-79184800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:79180800-79182800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:79180800-79182800	Enhancers	HSMMtube	muscle
8	chr1:79181400-79182600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:79181400-79183600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:79181400-79184200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:79181600-79183000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:79181800-79182800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:79181800-79184200	Weak transcription	HSMM	muscle
14	chr1:79182000-79184000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:79182400-79182800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:79182400-79182800	Enhancers	HUVEC	blood vessel

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

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