Variant report

Variant	rs11225308
Chromosome Location	chr11:102399478-102399479
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10502001	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10895306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10895307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10895308	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11225303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11225304	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11225307	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11225309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs14983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[ASN][1000 genomes]
rs17098292	0.95[YRI][hapmap]
rs17352054	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs2156528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2187364	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2408390	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7926218	0.92[YRI][hapmap]

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	nsv1035567	chr11:102264516-102431607	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv469990	chr11:102335609-102413943	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv556150	chr11:102335609-102415859	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv468854	chr11:102336617-102413943	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv556151	chr11:102336617-102413943	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11225308	BIRC2	cis	parietal	SCAN
rs11225308	CCDC82	trans	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102393400-102401200	Weak transcription	Pancreas	Pancrea
2	chr11:102394000-102401200	Weak transcription	Primary B cells from peripheral blood	blood
3	chr11:102397800-102399800	Enhancers	A549	lung
4	chr11:102398200-102399600	Enhancers	Hela-S3	cervix
5	chr11:102398200-102400000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr11:102398200-102400000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:102398200-102400200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:102398400-102400000	Enhancers	HMEC	breast
9	chr11:102398400-102400200	Enhancers	NHEK	skin
10	chr11:102399000-102399600	Enhancers	NH-A	brain
11	chr11:102399000-102400200	Enhancers	Brain Substantia Nigra	brain
12	chr11:102399000-102400800	Weak transcription	HUVEC	blood vessel
13	chr11:102399000-102401000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr11:102399200-102400000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr11:102399400-102400400	Enhancers	Brain Hippocampus Middle	brain
16	chr11:102399400-102401200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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