Variant report

Variant	rs1368092
Chromosome Location	chr2:134290524-134290525
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:134288676..134290659-chr2:134294672..134296438,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10170172	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1017365	0.88[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11682672	0.88[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1368093	0.89[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs1368094	0.95[EUR][1000 genomes]
rs1432285	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1432286	0.88[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1432287	0.89[CEU][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1816384	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1816385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1835816	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1835817	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1897427	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1897432	0.82[TSI][hapmap]
rs6430424	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6711103	0.89[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6731024	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs6737047	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6750306	0.82[TSI][hapmap]
rs6755693	0.82[CEU][hapmap];0.91[GIH][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs930195	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]

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	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv2830192	chr2:134259612-134311713	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1006101	chr2:134263288-134973917	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1368092	COX6B2	trans	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134282600-134299200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:134285000-134290800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:134286200-134311600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:134286600-134290600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:134289600-134290600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:134289600-134290600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:134289800-134291000	Enhancers	HMEC	breast
8	chr2:134290000-134290600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr2:134290000-134290800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:134290000-134291000	Enhancers	Hela-S3	cervix
11	chr2:134290000-134291200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:134290000-134291200	Enhancers	NHEK	skin
13	chr2:134290200-134291000	Enhancers	Muscle Satellite Cultured Cells	--
14	chr2:134290400-134291000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:134290400-134291000	Enhancers	Osteobl	bone

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