Variant report

Variant	rs4908290
Chromosome Location	chr1:103551498-103551499
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1012281	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10493986	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874669	1.00[CHB][hapmap]
rs10874678	0.81[AMR][1000 genomes]
rs10874679	0.84[CEU][hapmap];0.85[AMR][1000 genomes]
rs11164640	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11164643	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11164663	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs11164664	0.93[ASN][1000 genomes]
rs11164665	0.87[ASW][hapmap];0.84[CEU][hapmap];0.91[MEX][hapmap];0.87[AMR][1000 genomes]
rs11164668	0.83[CEU][hapmap];0.82[AMR][1000 genomes]
rs11164669	0.92[CEU][hapmap];0.82[AMR][1000 genomes]
rs11586849	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12062184	1.00[CHB][hapmap]
rs12064766	1.00[CHB][hapmap]
rs12084902	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12117071	1.00[CHB][hapmap]
rs12118250	1.00[CHB][hapmap]
rs12121498	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12121824	1.00[CHB][hapmap]
rs12121894	1.00[CHB][hapmap]
rs12126868	1.00[CHB][hapmap]
rs12130285	1.00[CHB][hapmap]
rs12130848	0.93[ASN][1000 genomes]
rs12133515	1.00[CHB][hapmap]
rs12135438	1.00[CHB][hapmap]
rs12141988	1.00[CHB][hapmap]
rs12145801	1.00[CHB][hapmap]
rs12145872	1.00[CHB][hapmap]
rs1337195	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415359	0.83[MEX][hapmap]
rs1415361	0.81[AMR][1000 genomes]
rs1415363	1.00[CHD][hapmap];0.96[GIH][hapmap]
rs1415364	0.84[CEU][hapmap];0.83[AMR][1000 genomes]
rs17127270	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2045819	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2376260	1.00[CHB][hapmap]
rs2376280	0.84[CEU][hapmap];0.82[MEX][hapmap];0.82[AMR][1000 genomes]
rs2376281	0.84[CEU][hapmap];0.82[AMR][1000 genomes]
rs3861742	1.00[CHB][hapmap]
rs4391683	1.00[CHB][hapmap]
rs4907986	0.81[AMR][1000 genomes]
rs4908286	0.84[CEU][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4908287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4908288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs7513552	1.00[CHB][hapmap]
rs7517160	0.93[ASN][1000 genomes]
rs7543082	1.00[CHB][hapmap]
rs9970114	0.84[CEU][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522922	chr1:103305021-103764640	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv871372	chr1:103403752-103564540	Strong transcription Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv830893	chr1:103458498-103635579	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv931600	chr1:103548397-104161031	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4908290	DBT	cis	cerebellum	SCAN
rs4908290	SNORD116-25	trans	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:103517400-103557200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:103522400-103559000	Weak transcription	HSMM	muscle
3	chr1:103539600-103556600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:103544000-103570400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:103544200-103551800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:103545000-103566800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:103546200-103556000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:103548000-103564400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:103551400-103552000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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