Variant report

Variant	rs2063245
Chromosome Location	chr5:90239911-90239912
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10078568	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1876633	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3105791	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3105792	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3114652	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3114654	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36131676	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4916696	0.92[ASN][1000 genomes]
rs4916697	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4916832	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6891672	0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats 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	58 gene(s)	inside rSNPs	diseases
2	nsv517049	chr5:90003131-90262475	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2063245	MCTP1	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90225800-90244000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr5:90230400-90265200	Weak transcription	K562	blood
3	chr5:90231600-90250800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:90236600-90243400	Weak transcription	HepG2	liver
5	chr5:90236800-90240000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:90236800-90263200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:90237400-90241000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:90237400-90246400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:90237600-90241600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:90237600-90241800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:90237600-90242200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:90237600-90245600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr5:90237800-90241600	Weak transcription	Brain Germinal Matrix	brain
14	chr5:90239200-90240600	Enhancers	NHEK	skin
15	chr5:90239400-90240200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:90239400-90240200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:90239400-90240400	Enhancers	A549	lung
18	chr5:90239800-90241000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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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

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