Variant report

Variant	rs11664013
Chromosome Location	chr18:12582788-12582789
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10048276	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1105748	1.00[CHD][hapmap]
rs11660232	1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11662531	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11663358	0.87[ASN][1000 genomes]
rs11664068	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11664219	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11664773	0.87[ASN][1000 genomes]
rs11665415	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11665542	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12961307	1.00[CHD][hapmap]
rs12965549	1.00[CHD][hapmap]
rs12971000	1.00[CHD][hapmap]
rs1592641	1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17524639	1.00[CHD][hapmap]
rs17525318	1.00[CHD][hapmap]
rs17525459	1.00[CHD][hapmap]
rs17525599	1.00[CHD][hapmap]
rs17595746	1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs17615525	1.00[CHD][hapmap]
rs17615801	1.00[CHD][hapmap]
rs17615991	1.00[CHD][hapmap]
rs1940973	1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2155699	0.87[ASN][1000 genomes]
rs2186906	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs28527375	0.87[ASN][1000 genomes]
rs28565322	0.87[ASN][1000 genomes]
rs28575715	0.87[ASN][1000 genomes]
rs28634564	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28663159	0.87[ASN][1000 genomes]
rs28815517	0.87[ASN][1000 genomes]
rs28821540	0.87[ASN][1000 genomes]
rs56029848	0.87[ASN][1000 genomes]
rs56870830	0.87[ASN][1000 genomes]
rs57706356	0.87[ASN][1000 genomes]
rs58638386	0.87[ASN][1000 genomes]
rs60563648	0.87[ASN][1000 genomes]
rs71351500	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73405602	0.87[ASN][1000 genomes]
rs73407510	0.87[ASN][1000 genomes]
rs73407511	0.87[ASN][1000 genomes]
rs73407524	0.87[ASN][1000 genomes]
rs919	1.00[CHD][hapmap]
rs9946557	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9953831	1.00[JPT][hapmap]
rs9959145	0.91[GIH][hapmap];0.87[ASN][1000 genomes]
rs9959201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9960706	1.00[ASN][1000 genomes]
rs9966118	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9967026	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9989546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][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	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11664013	SLMO1	cis	Thyroid	GTEx
rs11664013	SLMO1	cis	Adipose Subcutaneous	GTEx
rs11664013	AP001029.1	cis	Artery Tibial	GTEx
rs11664013	SPIRE1	cis	multi-tissue	Pritchard
rs11664013	SLMO1	cis	Artery Tibial	GTEx
rs11664013	RP11-861E21.1	cis	Artery Tibial	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12570000-12595600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr18:12578800-12588600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr18:12579400-12588800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr18:12582000-12583200	Enhancers	HepG2	liver
5	chr18:12582200-12585400	Weak transcription	Fetal Stomach	stomach

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