Variant report

Variant	rs11656106
Chromosome Location	chr17:16854385-16854386
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11078356	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs11651187	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs11652811	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11652843	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11654088	0.81[CEU][hapmap]
rs11654431	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs12937629	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12950077	0.86[ASN][1000 genomes]
rs17793572	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs34562485	0.86[ASN][1000 genomes]
rs34650767	0.86[ASN][1000 genomes]
rs34932194	0.86[ASN][1000 genomes]
rs35286584	0.86[ASN][1000 genomes]
rs35529291	0.86[ASN][1000 genomes]
rs35612151	1.00[ASN][1000 genomes]
rs35614113	0.86[ASN][1000 genomes]
rs35655892	0.86[ASN][1000 genomes]
rs35830162	0.86[ASN][1000 genomes]
rs4343329	0.85[CEU][hapmap]
rs4517836	0.80[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4985724	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4985725	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4985735	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4985783	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58928848	0.82[EUR][1000 genomes]
rs6502540	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71362292	0.86[ASN][1000 genomes]
rs7209074	0.81[AMR][1000 genomes]
rs7216399	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7222430	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7223652	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7224182	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7225292	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7225344	0.84[CEU][hapmap]
rs8065836	1.00[JPT][hapmap]
rs8072293	0.80[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8075444	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8081126	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs9889948	0.81[AMR][1000 genomes];0.81[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	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv833379	chr17:16683585-16859539	Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1055688	chr17:16800788-16868860	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1058863	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv543227	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv907726	chr17:16821204-16875636	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11656106	LOC96597	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16852000-16857000	ZNF genes & repeats	GM12878-XiMat	blood
2	chr17:16852800-16857000	Weak transcription	Brain Hippocampus Middle	brain
3	chr17:16853000-16856400	Strong transcription	Primary B cells from peripheral blood	blood
4	chr17:16853000-16856800	Weak transcription	Primary B cells from cord blood	blood
5	chr17:16853000-16858800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr17:16854000-16854600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr17:16854000-16855600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr17:16854200-16855600	Weak transcription	Spleen	Spleen

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