Variant report

Variant	rs10788606
Chromosome Location	chr10:90297927-90297928
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10430643	0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10430716	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11202769	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11202772	0.95[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12219242	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12247690	0.82[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap]
rs12249510	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1325905	0.82[JPT][hapmap]
rs1952122	0.83[ASW][hapmap]
rs2477958	0.83[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2576160	0.82[ASN][1000 genomes]
rs2576161	0.82[ASN][1000 genomes]
rs2576164	0.83[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs6586140	0.91[CHB][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7901991	0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7904690	0.81[JPT][hapmap]
rs9664314	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948664	chr10:90076715-90517150	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv825500	chr10:90221443-90302503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv533167	chr10:90236197-90341481	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv430254	chr10:90265420-90500520	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10788606	RNLS	cis	cerebellum	SCAN
rs10788606	BTAF1	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90294800-90298000	Weak transcription	Liver	Liver
2	chr10:90296000-90299800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr10:90296200-90298200	Enhancers	Fetal Lung	lung
4	chr10:90296400-90298800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr10:90296400-90302400	Enhancers	HSMMtube	muscle
6	chr10:90296600-90301800	Enhancers	HSMM	muscle
7	chr10:90296600-90302000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr10:90296600-90309200	Weak transcription	Psoas Muscle	Psoas
9	chr10:90296800-90298400	Enhancers	Muscle Satellite Cultured Cells	--
10	chr10:90297000-90298200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr10:90297200-90298000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr10:90297200-90298400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr10:90297200-90298400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr10:90297200-90300400	Enhancers	Fetal Kidney	kidney
15	chr10:90297400-90298200	Enhancers	NHLF	lung
16	chr10:90297400-90298600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr10:90297400-90298800	Enhancers	Adipose Nuclei	Adipose
18	chr10:90297600-90298200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr10:90297800-90298200	Enhancers	Hela-S3	cervix
20	chr10:90297800-90298200	Enhancers	NHDF-Ad	bronchial

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