Variant report

Variant	rs1320632
Chromosome Location	chr11:102596063-102596064
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1276271	1.00[YRI][hapmap]
rs1276273	0.87[AMR][1000 genomes]
rs1276282	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1291326	0.87[AMR][1000 genomes]
rs1291327	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1939011	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1939018	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1939020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1940479	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1940481	0.91[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs2155052	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2509010	0.82[YRI][hapmap]
rs2701988	0.91[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2701994	0.91[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2846356	0.87[AMR][1000 genomes]
rs2846363	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2846364	0.91[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2846702	0.91[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2846706	0.87[AMR][1000 genomes]
rs2846707	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6590984	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7121624	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs948217	0.90[CEU][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832252	chr11:102445479-102627879	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1037454	chr11:102487521-102601233	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv541156	chr11:102487521-102601233	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1320632	CNTN5	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102592400-102596200	Enhancers	Monocytes-CD14+_RO01746	blood
2	chr11:102593600-102598800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:102594600-102596400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr11:102594600-102597600	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr11:102594600-102598200	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr11:102595400-102596800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr11:102595400-102597200	Enhancers	HMEC	breast
8	chr11:102595600-102596600	Enhancers	Brain Substantia Nigra	brain
9	chr11:102595600-102596800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr11:102595600-102596800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:102595800-102596600	Enhancers	Brain Anterior Caudate	brain
12	chr11:102595800-102596600	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr11:102595800-102596600	Enhancers	NHEK	skin
14	chr11:102595800-102598200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr11:102596000-102596400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:102596000-102596400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:102596000-102596400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr11:102596000-102596600	Enhancers	Brain Hippocampus Middle	brain

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