Variant report

Variant	rs11693248
Chromosome Location	chr2:96884553-96884554
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:96877772..96879373-chr2:96883680..96885958,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1030864	0.83[EUR][1000 genomes]
rs1168968	0.83[EUR][1000 genomes]
rs1168970	0.83[EUR][1000 genomes]
rs1168972	0.83[EUR][1000 genomes]
rs1168974	0.83[EUR][1000 genomes]
rs1168975	0.83[EUR][1000 genomes]
rs1168976	0.83[EUR][1000 genomes]
rs1724125	0.81[EUR][1000 genomes]
rs2301707	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3821051	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4907230	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58448550	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772154	0.80[AMR][1000 genomes]
rs772175	0.84[AMR][1000 genomes]
rs772178	0.84[AMR][1000 genomes]
rs810057	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	esv3435047	chr2:96836850-96890437	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
9	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
10	nsv963665	chr2:96882253-96905611	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11693248	CIAO1	Cis_1M	lymphoblastoid	RTeQTL
rs11693248	GPAT2	cis	Muscle Skeletal	GTEx
rs11693248	ADRA2B	cis	Thyroid	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96875000-96906200	Weak transcription	Esophagus	oesophagus
2	chr2:96875200-96905000	Weak transcription	Aorta	Aorta
3	chr2:96875600-96907000	Weak transcription	Fetal Thymus	thymus
4	chr2:96875800-96891000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:96875800-96905800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:96876000-96885400	Weak transcription	Psoas Muscle	Psoas
7	chr2:96876000-96885600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:96876000-96885800	Weak transcription	Pancreas	Pancrea
9	chr2:96876000-96896200	Weak transcription	Left Ventricle	heart
10	chr2:96876000-96902400	Weak transcription	Fetal Intestine Large	intestine
11	chr2:96876000-96904200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:96876000-96905800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:96876000-96906600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr2:96876000-96915200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr2:96876200-96885600	Weak transcription	Fetal Heart	heart
16	chr2:96876200-96885800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:96876200-96886600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:96876200-96886600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:96876200-96888800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr2:96876200-96891400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr2:96876200-96893400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:96876200-96895800	Weak transcription	Lung	lung
23	chr2:96876200-96903200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:96876200-96903600	Weak transcription	Gastric	stomach
25	chr2:96876200-96905200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:96876200-96906000	Weak transcription	Osteobl	bone
27	chr2:96876200-96906600	Weak transcription	Brain Anterior Caudate	brain
28	chr2:96876200-96916000	Weak transcription	Dnd41	blood
29	chr2:96876200-96917800	Weak transcription	Brain Angular Gyrus	brain
30	chr2:96876400-96885600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr2:96876400-96890600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:96876400-96891000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:96876600-96902600	Weak transcription	HepG2	liver
34	chr2:96877800-96916000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:96878000-96885400	Weak transcription	Fetal Intestine Small	intestine
36	chr2:96878000-96891000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:96878600-96891000	Weak transcription	Fetal Muscle Leg	muscle
38	chr2:96878800-96890200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:96879600-96902400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr2:96879600-96903200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:96879600-96903200	Weak transcription	Fetal Stomach	stomach
42	chr2:96881600-96890800	Weak transcription	Primary B cells from cord blood	blood
43	chr2:96882200-96885000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr2:96883800-96888000	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr2:96883800-96888000	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr2:96884200-96884600	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr2:96884200-96884800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:96884200-96884800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr2:96884400-96886600	Enhancers	Skeletal Muscle Female	skeletal muscle

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