Variant report

Variant	rs3105791
Chromosome Location	chr5:90226542-90226543
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10078568	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1876633	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2063245	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap]
rs3105792	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3114652	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3114654	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36131676	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4916696	0.94[ASN][1000 genomes]
rs4916697	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4916832	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs57258230	0.85[EUR][1000 genomes]
rs60681604	0.81[EUR][1000 genomes]

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
rs3105791	MCTP1	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90185000-90226600	Weak transcription	K562	blood
2	chr5:90208000-90231000	Weak transcription	Brain Anterior Caudate	brain
3	chr5:90225600-90226600	Enhancers	Liver	Liver
4	chr5:90225600-90226800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:90225600-90229600	Weak transcription	Placenta	Placenta
6	chr5:90225600-90232400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:90225800-90226800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr5:90225800-90228400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:90225800-90230200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:90225800-90236200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:90225800-90244000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr5:90226000-90228200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:90226200-90226800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:90226200-90227800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr5:90226200-90228400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr5:90226200-90228800	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr5:90226400-90226800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr5:90226400-90226800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr5:90226400-90226800	Enhancers	A549	lung

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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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