Variant report

Variant	rs11123790
Chromosome Location	chr2:100271619-100271620
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:100271470..100273673-chr2:100282550..100284543,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10167554	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11684088	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12620982	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12712049	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12712054	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13029690	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1357719	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1996984	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2030691	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2030692	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2030693	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2049400	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2177541	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2177542	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2309729	0.83[EUR][1000 genomes]
rs2871316	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3792129	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3792130	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3792131	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4332968	0.80[EUR][1000 genomes]
rs4850910	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4851220	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4851221	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6542884	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6738724	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6745568	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6746146	0.81[EUR][1000 genomes]
rs7561009	0.83[EUR][1000 genomes]
rs7579222	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs868665	0.81[EUR][1000 genomes]
rs9284724	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9308826	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9308827	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9678859	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1003343	chr2:100241560-100848900	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv535843	chr2:100241560-100848900	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100253200-100308800	Weak transcription	Gastric	stomach
2	chr2:100255400-100285400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:100255400-100285400	Weak transcription	Dnd41	blood
4	chr2:100257600-100308600	Weak transcription	Thymus	Thymus
5	chr2:100259400-100274600	Weak transcription	Primary T cells from cord blood	blood
6	chr2:100260200-100283600	Strong transcription	Primary B cells from peripheral blood	blood
7	chr2:100260800-100274400	Weak transcription	Right Atrium	heart
8	chr2:100261400-100279000	Weak transcription	Fetal Kidney	kidney
9	chr2:100264000-100328600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr2:100264200-100281800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:100266200-100273400	Weak transcription	Fetal Heart	heart
12	chr2:100266400-100277200	Weak transcription	Brain Germinal Matrix	brain
13	chr2:100268400-100272200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:100268400-100287800	Strong transcription	Primary B cells from cord blood	blood
15	chr2:100268800-100282400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:100269000-100273400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:100269200-100288800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:100269600-100273400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:100269600-100273600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:100269600-100275400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:100269600-100280200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:100269800-100271800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:100269800-100277200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:100270000-100278800	Weak transcription	NH-A	brain
25	chr2:100270200-100273400	Weak transcription	Left Ventricle	heart
26	chr2:100270200-100274400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:100270200-100275600	Weak transcription	Lung	lung
28	chr2:100270800-100272000	Enhancers	Brain Anterior Caudate	brain
29	chr2:100271000-100271800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:100271000-100271800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:100271000-100272000	Enhancers	Brain Cingulate Gyrus	brain
32	chr2:100271200-100272000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:100271200-100272200	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr2:100271200-100272200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:100271400-100272000	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr2:100271400-100272000	Enhancers	Fetal Brain Male	brain
37	chr2:100271400-100272400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:100271400-100273400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:100271400-100273600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:100271600-100271800	Enhancers	Esophagus	oesophagus
41	chr2:100271600-100273200	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:100271600-100279400	Weak transcription	Brain Substantia Nigra	brain
43	chr2:100271600-100280200	Weak transcription	Fetal Brain Female	brain

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