Variant report

Variant	rs13106409
Chromosome Location	chr4:90973406-90973407
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10516857	0.96[EUR][1000 genomes]
rs10516858	0.82[CEU][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs10516860	0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10516862	0.89[EUR][1000 genomes]
rs12500465	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12639636	0.90[EUR][1000 genomes]
rs12642395	0.88[EUR][1000 genomes]
rs12642404	0.88[EUR][1000 genomes]
rs12647171	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12647266	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12648872	0.80[EUR][1000 genomes]
rs12649987	0.89[EUR][1000 genomes]
rs12650363	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12651123	0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs13107286	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13108338	0.89[EUR][1000 genomes]
rs13113863	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13119778	0.94[EUR][1000 genomes]
rs13121853	0.88[EUR][1000 genomes]
rs13124133	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13131070	0.88[EUR][1000 genomes]
rs13131903	0.81[EUR][1000 genomes]
rs13148977	0.96[EUR][1000 genomes]
rs13149395	0.85[EUR][1000 genomes]
rs13150124	0.88[EUR][1000 genomes]
rs13151441	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1443796	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1443798	0.95[EUR][1000 genomes]
rs1562034	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17808648	0.88[EUR][1000 genomes]
rs17808829	0.80[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs1982293	0.88[EUR][1000 genomes]
rs2120372	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2120375	0.81[EUR][1000 genomes]
rs34064092	0.88[EUR][1000 genomes]
rs34343229	0.88[EUR][1000 genomes]
rs34886505	0.86[EUR][1000 genomes]
rs35197902	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3822098	0.88[JPT][hapmap]
rs55663876	0.88[EUR][1000 genomes]
rs55686873	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62312738	0.88[EUR][1000 genomes]
rs62312743	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6532212	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6532213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814978	0.98[EUR][1000 genomes]
rs6819755	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6830014	0.82[CHB][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes]
rs6837222	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs723992	1.00[CEU][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs7660182	0.88[EUR][1000 genomes]
rs7661577	0.96[EUR][1000 genomes]
rs7685355	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv470053	chr4:90879613-91439573	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv879537	chr4:90883047-91165346	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv931074	chr4:90970476-91753697	Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv830006	chr4:90971656-91186340	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13106409	DSPP	cis	cerebellum	SCAN
rs13106409	FAM190A	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90973200-90973600	Enhancers	H9 Cell Line	embryonic stem cell
2	chr4:90973200-90974200	Enhancers	H1 Cell Line	embryonic stem cell
3	chr4:90973200-90974200	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr4:90973400-90973800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
5	chr4:90973400-90974000	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr4:90973400-90974200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:90973400-90974200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:90973400-90974200	Enhancers	Brain Germinal Matrix	brain
9	chr4:90973400-90974400	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr4:90973400-90974600	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr4:90973400-90974800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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