Variant report

Variant	rs10935478
Chromosome Location	chr3:98428155-98428156
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10935473	0.91[EUR][1000 genomes]
rs10935480	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13065271	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4857414	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73133996	0.96[AMR][1000 genomes];0.96[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	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv524042	chr3:98317836-98436188	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1003922	chr3:98410967-98453602	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv536662	chr3:98410967-98453602	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10935478	ST3GAL6-AS1	cis	Heart Left Ventricle	GTEx
rs10935478	ST3GAL6-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs10935478	ST3GAL6-AS1	cis	Thyroid	GTEx
rs10935478	ST3GAL6-AS1	cis	Nerve Tibial	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98424600-98428600	Weak transcription	Adipose Nuclei	Adipose
2	chr3:98424600-98430200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr3:98425000-98428600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:98425000-98431600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:98425600-98438600	Weak transcription	Aorta	Aorta
6	chr3:98426800-98428400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr3:98427200-98428400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:98427200-98430200	Enhancers	Fetal Muscle Leg	muscle
9	chr3:98427400-98429600	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr3:98427400-98430400	Enhancers	Fetal Stomach	stomach
11	chr3:98427400-98432800	Enhancers	Placenta	Placenta
12	chr3:98427600-98428200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr3:98427600-98428800	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr3:98427600-98429000	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr3:98427600-98429000	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr3:98427600-98429200	Enhancers	Fetal Lung	lung
17	chr3:98427600-98429400	Enhancers	Ovary	ovary
18	chr3:98427600-98429600	Enhancers	Fetal Kidney	kidney
19	chr3:98427800-98428200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:98427800-98428800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:98427800-98429400	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr3:98428000-98428800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:98428000-98429000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:98428000-98429400	Enhancers	HUVEC	blood vessel

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