Variant report

Variant	rs11654088
Chromosome Location	chr17:16849813-16849814
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11656106	0.81[CEU][hapmap]
rs12603019	0.91[ASN][1000 genomes]
rs12604041	0.87[ASN][1000 genomes]
rs3892371	0.91[ASN][1000 genomes]
rs4985724	0.85[CEU][hapmap]
rs4985725	0.85[CEU][hapmap]
rs4985735	0.85[CEU][hapmap]
rs4985783	0.85[CEU][hapmap]
rs55703181	0.88[ASN][1000 genomes]
rs56399647	0.88[ASN][1000 genomes]
rs7216399	0.85[CEU][hapmap]
rs72637382	0.85[ASN][1000 genomes]
rs72637383	0.87[ASN][1000 genomes]
rs72637384	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	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
rs11654088	LOC96597	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16844200-16852000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr17:16846400-16850400	Enhancers	Brain Hippocampus Middle	brain
3	chr17:16846400-16851600	Enhancers	Brain Cingulate Gyrus	brain
4	chr17:16846600-16852000	Genic enhancers	Primary B cells from peripheral blood	blood
5	chr17:16847400-16850400	Genic enhancers	GM12878-XiMat	blood
6	chr17:16847800-16851600	Enhancers	Primary B cells from cord blood	blood
7	chr17:16848600-16850400	Enhancers	Brain Angular Gyrus	brain
8	chr17:16848600-16851800	Enhancers	Brain Substantia Nigra	brain
9	chr17:16849400-16850200	Weak transcription	A549	lung
10	chr17:16849400-16850600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr17:16849600-16851600	Weak transcription	Spleen	Spleen
12	chr17:16849800-16851200	Weak transcription	Brain Anterior Caudate	brain
13	chr17:16849800-16851400	Weak transcription	Brain Inferior Temporal Lobe	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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