Variant report

Variant	rs2923125
Chromosome Location	chr11:10398193-10398194
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	chr11:10397046..10398649-chr11:10399369..10401116,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10770108	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11042769	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11042770	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11042772	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12365418	0.80[AFR][1000 genomes]
rs1597448	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1597449	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16907747	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2198008	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2198009	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2198010	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2403305	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2403306	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2923085	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2923086	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2923087	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2923088	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2923115	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2923116	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2923117	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2923120	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2923121	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2923122	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2923124	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2957658	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2957664	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2957665	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2957666	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2957667	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2957668	0.89[ASN][1000 genomes]
rs2957669	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2957670	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2957675	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2957677	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2957678	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2957679	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910129	0.81[ASN][1000 genomes]
rs5015228	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6416051	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7112833	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7117816	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7117951	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7934497	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2923125	SNORA23	cis	cerebellum	SCAN
rs2923125	RPL27A	cis	parietal	SCAN
rs2923125	OLFML1	cis	cerebellum	SCAN
rs2923125	SYT9	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10388800-10401400	Weak transcription	Esophagus	oesophagus
2	chr11:10389000-10401400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr11:10389000-10401600	Weak transcription	Right Atrium	heart
4	chr11:10391800-10403800	Enhancers	Adipose Nuclei	Adipose
5	chr11:10392800-10403000	Enhancers	NHLF	lung
6	chr11:10394600-10402200	Enhancers	NHDF-Ad	bronchial
7	chr11:10394600-10403000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr11:10394800-10398400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr11:10394800-10398400	Enhancers	Colon Smooth Muscle	Colon
10	chr11:10394800-10399200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr11:10394800-10399400	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr11:10395200-10400600	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr11:10395200-10401400	Weak transcription	Left Ventricle	heart
14	chr11:10395200-10401400	Weak transcription	Lung	lung
15	chr11:10395800-10399600	Enhancers	Muscle Satellite Cultured Cells	--
16	chr11:10396000-10398400	Enhancers	Ovary	ovary
17	chr11:10396200-10398600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:10396200-10398600	Enhancers	Fetal Muscle Leg	muscle
19	chr11:10396200-10399600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr11:10396400-10400200	Weak transcription	Spleen	Spleen
21	chr11:10396600-10398200	Enhancers	HSMM	muscle
22	chr11:10396600-10399400	Enhancers	HSMMtube	muscle
23	chr11:10397200-10398400	Enhancers	Fetal Muscle Trunk	muscle
24	chr11:10397400-10401200	Weak transcription	NHEK	skin
25	chr11:10397400-10401400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr11:10398000-10399200	Weak transcription	Psoas Muscle	Psoas
27	chr11:10398000-10399200	Weak transcription	NH-A	brain
28	chr11:10398000-10400000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr11:10398000-10401400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr11:10398000-10401400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr11:10398000-10401600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr11:10398000-10403800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:10398000-10404000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr11:10398000-10404000	Enhancers	Osteobl	bone

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