Variant report

Variant	rs10757004
Chromosome Location	chr9:18940950-18940951
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1006120	0.83[CHB][hapmap]
rs10757007	1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]
rs10757008	1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]
rs10757009	0.87[ASN][1000 genomes]
rs10757010	0.87[ASN][1000 genomes]
rs10757011	0.95[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs10757016	0.95[CHB][hapmap]
rs10757018	0.90[CHB][hapmap]
rs10757020	0.81[CHB][hapmap]
rs10757022	0.81[CHD][hapmap]
rs10811069	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10811075	0.82[CHB][hapmap]
rs10811080	0.83[CHB][hapmap];0.88[CHD][hapmap]
rs10811082	0.83[CHB][hapmap]
rs10811085	0.87[CHB][hapmap]
rs10811092	0.86[CHB][hapmap]
rs10811099	0.91[CHB][hapmap];0.86[CHD][hapmap]
rs10963863	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs10963869	0.83[ASN][1000 genomes]
rs10963896	0.87[CHB][hapmap]
rs10963897	0.82[CHB][hapmap]
rs10963898	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs10963907	0.91[CHB][hapmap];0.86[CHD][hapmap]
rs10963910	0.86[CHB][hapmap]
rs10963911	0.86[CHB][hapmap]
rs10963912	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs11790123	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs12352657	0.83[CHB][hapmap]
rs12352756	0.83[CHB][hapmap]
rs12553946	0.91[CHB][hapmap]
rs1327502	0.82[ASN][1000 genomes]
rs17236081	0.91[CHB][hapmap];0.84[CHD][hapmap]
rs1887444	1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]
rs1887445	0.87[ASN][1000 genomes]
rs1932452	0.91[CHB][hapmap]
rs1932453	0.91[CHB][hapmap]
rs1977444	0.95[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs2039008	0.83[CHB][hapmap]
rs2039010	0.83[CHB][hapmap]
rs2152464	0.81[CHB][hapmap];0.86[CHD][hapmap]
rs3892045	0.91[CHB][hapmap];0.86[CHD][hapmap]
rs4395970	0.95[CHB][hapmap]
rs4506313	0.83[CHB][hapmap]
rs4977273	0.83[CHB][hapmap];0.84[CHD][hapmap]
rs4977476	0.95[CHB][hapmap];0.83[CHD][hapmap];0.84[ASN][1000 genomes]
rs4977477	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs4977479	0.83[ASN][1000 genomes]
rs6475272	0.87[CHB][hapmap]
rs6475273	0.87[CHB][hapmap]
rs6475274	0.82[CHB][hapmap]
rs6475275	0.83[CHB][hapmap]
rs6475276	0.83[CHB][hapmap]
rs6475279	0.85[CHB][hapmap]
rs6475295	0.87[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs6475296	0.82[CHD][hapmap]
rs7021572	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]
rs7024697	0.87[CHB][hapmap]
rs7025123	0.82[CHB][hapmap]
rs7028706	0.82[CHB][hapmap]
rs7028858	0.87[CHB][hapmap]
rs7028936	0.87[CHB][hapmap]
rs7037837	0.87[CHB][hapmap]
rs7038730	0.87[CHB][hapmap];0.88[CHD][hapmap]
rs7044864	0.91[CHB][hapmap];0.84[CHD][hapmap]
rs7045059	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7045203	0.86[CHB][hapmap]
rs7048198	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7848918	0.83[CHB][hapmap]
rs7849807	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7852907	0.86[CHB][hapmap]
rs7856117	0.87[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs7857590	0.87[CHB][hapmap];0.88[CHD][hapmap]
rs7862694	0.91[CHB][hapmap];0.86[CHD][hapmap]
rs7864376	0.87[CHB][hapmap];0.86[CHD][hapmap]
rs7865237	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7865461	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7867428	0.82[CHB][hapmap]
rs7871205	0.81[CHB][hapmap]
rs7871456	0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs883439	0.91[CHB][hapmap];0.86[CHD][hapmap]
rs945445	0.86[JPT][hapmap]
rs953734	0.83[CHB][hapmap];0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv892692	chr9:18519699-19045502	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv949111	chr9:18758205-18994588	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
7	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
8	nsv466282	chr9:18920357-18960393	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv471289	chr9:18920357-18960393	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv613727	chr9:18920357-18960393	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10757004	C9orf53	cis	parietal	SCAN
rs10757004	PSIP1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18939400-18941000	Enhancers	Stomach Mucosa	stomach
2	chr9:18939600-18941000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr9:18940600-18942000	Enhancers	Fetal Lung	lung
4	chr9:18940600-18943200	Enhancers	Fetal Heart	heart
5	chr9:18940800-18941800	Weak transcription	Lung	lung
6	chr9:18940800-18942400	Weak transcription	Left Ventricle	heart

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