Variant report

Variant	rs1339563
Chromosome Location	chr1:184503803-184503804
allele	A/G
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	0.88[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10737253	0.83[ASN][1000 genomes]
rs10797971	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10797972	0.88[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10797974	0.82[EUR][1000 genomes]
rs10797977	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10911606	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11588922	0.92[ASN][1000 genomes]
rs12125349	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12127674	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1339564	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339565	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1339566	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1339567	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1416752	0.92[CEU][hapmap];0.82[CHD][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs1569842	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1884200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2001270	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2038307	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2038308	0.88[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2144294	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2180073	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2180077	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2207528	0.83[ASN][1000 genomes]
rs2378888	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2890014	0.83[EUR][1000 genomes]
rs2890015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650667	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651208	0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4651210	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4651211	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4651213	0.89[CEU][hapmap];0.82[CHD][hapmap];0.85[TSI][hapmap]
rs4651216	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4651217	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4651218	0.83[EUR][1000 genomes]
rs4651219	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55729410	0.83[ASN][1000 genomes]
rs6661707	0.80[ASN][1000 genomes]
rs6666704	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7517518	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7533466	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7544240	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9970984	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9970990	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[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:69 , 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	chr1:184481400-184504000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:184483400-184504000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:184484000-184504000	Weak transcription	NHLF	lung
7	chr1:184485800-184504400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:184486800-184505400	Weak transcription	Fetal Intestine Large	intestine
9	chr1:184489800-184505400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:184495000-184504000	Weak transcription	Ovary	ovary
11	chr1:184500800-184504400	Enhancers	Psoas Muscle	Psoas
12	chr1:184501000-184504000	Weak transcription	Stomach Mucosa	stomach
13	chr1:184501000-184505200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:184501400-184504600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:184501400-184505400	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr1:184501800-184510200	Weak transcription	NHEK	skin
17	chr1:184502000-184504200	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr1:184502000-184504400	Enhancers	Right Atrium	heart
19	chr1:184502200-184504000	Enhancers	Spleen	Spleen
20	chr1:184502200-184504200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:184502200-184504400	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr1:184502200-184504400	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr1:184502200-184505000	Enhancers	Colon Smooth Muscle	Colon
24	chr1:184502200-184505000	Enhancers	Fetal Muscle Leg	muscle
25	chr1:184502400-184504000	Weak transcription	Right Ventricle	heart
26	chr1:184502400-184504200	Enhancers	Brain Angular Gyrus	brain
27	chr1:184502400-184504800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:184502400-184505400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:184502400-184517000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:184502400-184520200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:184502600-184504000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr1:184502600-184505200	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr1:184502600-184527200	Weak transcription	Fetal Brain Female	brain
34	chr1:184502800-184504400	Enhancers	Small Intestine	intestine
35	chr1:184502800-184504400	Enhancers	Stomach Smooth Muscle	stomach
36	chr1:184502800-184504800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:184502800-184505000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:184503000-184504000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:184503000-184504200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:184503000-184504200	Enhancers	Brain Anterior Caudate	brain
41	chr1:184503000-184504200	Weak transcription	Brain Hippocampus Middle	brain
42	chr1:184503000-184504400	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr1:184503000-184505200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr1:184503000-184505400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:184503000-184505400	Weak transcription	Fetal Muscle Trunk	muscle
46	chr1:184503200-184504000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:184503200-184504200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr1:184503200-184505000	Enhancers	Brain Substantia Nigra	brain
49	chr1:184503200-184505400	Weak transcription	Left Ventricle	heart
50	chr1:184503200-184505400	Weak transcription	Lung	lung

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