Variant report

Variant	rs10460375
Chromosome Location	chr2:183446892-183446893
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10166852	0.83[EUR][1000 genomes]
rs10460376	0.86[EUR][1000 genomes]
rs10497605	0.83[MEX][hapmap]
rs1527881	0.85[EUR][1000 genomes]
rs1527882	0.83[EUR][1000 genomes]
rs1594305	0.83[MEX][hapmap]
rs1965090	0.84[ASN][1000 genomes]
rs1978650	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1997240	0.85[EUR][1000 genomes]
rs4146244	0.85[EUR][1000 genomes]
rs5022567	0.83[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	nsv533782	chr2:183059730-183500040	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh 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	35 gene(s)	inside rSNPs	diseases
3	esv2830429	chr2:183300759-183545378	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv2757842	chr2:183437700-183835084	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2759104	chr2:183437700-183835084	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv875479	chr2:183442443-183482466	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv875480	chr2:183442443-183489249	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10460375	NEUROD1	cis	cerebellum	SCAN
rs10460375	PDE1A	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183442400-183447000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:183445400-183447000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:183445600-183447000	Enhancers	Osteobl	bone
4	chr2:183445800-183447000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:183446400-183451000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:183446800-183451200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:183446800-183451800	Weak transcription	Muscle Satellite Cultured Cells	--

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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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