Variant report

Variant	rs1339564
Chromosome Location	chr1:184504030-184504031
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:184493911..184496906-chr1:184501930..184505851,3	K562	blood:
2	chr1:184501312..184504109-chr1:184512326..184514186,2	MCF-7	breast:
3	chr1:184496059..184498642-chr1:184502199..184505203,5	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1007224	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10737253	0.83[ASN][1000 genomes]
rs10797971	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10797972	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10797974	0.83[EUR][1000 genomes]
rs10797977	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10911606	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11588922	0.92[ASN][1000 genomes]
rs12125349	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12127674	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1339563	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339565	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1339566	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1339567	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1416752	0.84[EUR][1000 genomes]
rs1569842	0.83[ASN][1000 genomes]
rs1884200	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2001270	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2038307	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2038308	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2144294	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2180073	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2180077	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2207528	0.83[ASN][1000 genomes]
rs2378888	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2890014	0.84[EUR][1000 genomes]
rs2890015	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650667	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651208	0.83[ASN][1000 genomes]
rs4651210	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4651211	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4651213	0.81[EUR][1000 genomes]
rs4651216	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4651217	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4651218	0.84[EUR][1000 genomes]
rs4651219	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55729410	0.83[ASN][1000 genomes]
rs6661707	0.80[ASN][1000 genomes]
rs6666704	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7517518	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7533466	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7544240	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9970984	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9970990	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184474400-184505400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:184478400-184505200	Weak transcription	Fetal Intestine Small	intestine
3	chr1:184480200-184505200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:184485800-184504400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:184486800-184505400	Weak transcription	Fetal Intestine Large	intestine
6	chr1:184489800-184505400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:184500800-184504400	Enhancers	Psoas Muscle	Psoas
8	chr1:184501000-184505200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:184501400-184504600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:184501400-184505400	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr1:184501800-184510200	Weak transcription	NHEK	skin
12	chr1:184502000-184504200	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr1:184502000-184504400	Enhancers	Right Atrium	heart
14	chr1:184502200-184504200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:184502200-184504400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:184502200-184504400	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr1:184502200-184505000	Enhancers	Colon Smooth Muscle	Colon
18	chr1:184502200-184505000	Enhancers	Fetal Muscle Leg	muscle
19	chr1:184502400-184504200	Enhancers	Brain Angular Gyrus	brain
20	chr1:184502400-184504800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:184502400-184505400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:184502400-184517000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:184502400-184520200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:184502600-184505200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr1:184502600-184527200	Weak transcription	Fetal Brain Female	brain
26	chr1:184502800-184504400	Enhancers	Small Intestine	intestine
27	chr1:184502800-184504400	Enhancers	Stomach Smooth Muscle	stomach
28	chr1:184502800-184504800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:184502800-184505000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:184503000-184504200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:184503000-184504200	Enhancers	Brain Anterior Caudate	brain
32	chr1:184503000-184504200	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:184503000-184504400	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr1:184503000-184505200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:184503000-184505400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:184503000-184505400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr1:184503200-184504200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr1:184503200-184505000	Enhancers	Brain Substantia Nigra	brain
39	chr1:184503200-184505400	Weak transcription	Left Ventricle	heart
40	chr1:184503200-184505400	Weak transcription	Lung	lung
41	chr1:184503200-184514600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:184503200-184516400	Weak transcription	Fetal Brain Male	brain
43	chr1:184503400-184504400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:184503400-184504400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:184503400-184504600	Weak transcription	Fetal Heart	heart
46	chr1:184503400-184504800	Enhancers	Fetal Stomach	stomach
47	chr1:184503400-184515800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr1:184503400-184520400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr1:184503600-184504200	Enhancers	NHDF-Ad	bronchial
50	chr1:184503800-184504200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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