Variant report

Variant	rs1524366
Chromosome Location	chr2:100279127-100279128
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:100279081..100281750-chr2:100284821..100286807,2	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]
rs10167100	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10182731	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10183116	0.87[EUR][1000 genomes]
rs10185240	0.87[EUR][1000 genomes]
rs10189976	0.87[EUR][1000 genomes]
rs10205134	0.87[EUR][1000 genomes]
rs11123791	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11123792	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11676683	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11901863	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12474603	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12712052	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1916959	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2030689	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2309728	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4325808	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4384839	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4410333	0.86[EUR][1000 genomes]
rs4611689	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4850908	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4850911	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4850912	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4850913	0.81[AMR][1000 genomes]
rs4851222	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6709165	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6719965	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6720070	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6734773	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7557598	0.87[EUR][1000 genomes]
rs7560182	0.87[EUR][1000 genomes]
rs7561948	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7566953	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs870560	0.87[EUR][1000 genomes]
rs9679019	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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:60 , 50 per page) page: 1 2

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	chr2:100260200-100283600	Strong transcription	Primary B cells from peripheral blood	blood
6	chr2:100264000-100328600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:100264200-100281800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:100268400-100287800	Strong transcription	Primary B cells from cord blood	blood
9	chr2:100268800-100282400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:100269200-100288800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:100269600-100280200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:100271600-100279400	Weak transcription	Brain Substantia Nigra	brain
13	chr2:100271600-100280200	Weak transcription	Fetal Brain Female	brain
14	chr2:100271800-100279200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:100272800-100281800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:100273200-100280800	Enhancers	Adipose Nuclei	Adipose
17	chr2:100274000-100279200	Weak transcription	Psoas Muscle	Psoas
18	chr2:100274000-100279200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:100274000-100279200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:100274000-100279400	Weak transcription	Fetal Lung	lung
21	chr2:100274000-100282000	Weak transcription	Aorta	Aorta
22	chr2:100274200-100297400	Weak transcription	Liver	Liver
23	chr2:100275800-100291000	Weak transcription	Lung	lung
24	chr2:100276400-100279800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:100276400-100279800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:100276400-100302000	Weak transcription	Left Ventricle	heart
27	chr2:100276600-100282400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:100276600-100284600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:100276600-100295800	Weak transcription	Right Atrium	heart
30	chr2:100276800-100281400	Weak transcription	Primary T cells from cord blood	blood
31	chr2:100277000-100280400	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr2:100277000-100281000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:100277400-100279200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:100277400-100279200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:100277600-100279400	Weak transcription	Brain Germinal Matrix	brain
36	chr2:100277600-100279600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:100277800-100279200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:100277800-100279200	Weak transcription	Ovary	ovary
39	chr2:100277800-100279400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr2:100277800-100282800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr2:100277800-100286400	Weak transcription	Pancreas	Pancrea
42	chr2:100278000-100285400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr2:100278200-100284800	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr2:100278400-100279800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:100278600-100280600	Enhancers	HSMMtube	muscle
46	chr2:100278600-100280600	Enhancers	Osteobl	bone
47	chr2:100278800-100280000	Enhancers	Brain Cingulate Gyrus	brain
48	chr2:100278800-100280200	Enhancers	Brain Hippocampus Middle	brain
49	chr2:100278800-100280400	Enhancers	HSMM	muscle
50	chr2:100278800-100280800	Enhancers	NH-A	brain

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