Variant report

Variant	rs1866388
Chromosome Location	chr5:142759785-142759786
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	chr5:142757061..142759968-chr5:142781467..142783841,2	K562	blood:
2	chr5:142758935..142760691-chr5:142768812..142770829,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113580	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10052957	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10482614	0.82[ASN][1000 genomes]
rs10482633	0.85[GIH][hapmap]
rs10482642	0.81[GIH][hapmap]
rs10482689	0.81[GIH][hapmap]
rs10515521	0.85[GIH][hapmap]
rs11740792	0.85[GIH][hapmap]
rs11747997	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11749561	1.00[JPT][hapmap]
rs1438732	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1635475	0.80[ASN][1000 genomes]
rs17339831	0.88[GIH][hapmap]
rs174048	0.95[ASN][1000 genomes]
rs174050	0.95[ASN][1000 genomes]
rs1837262	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs190488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2043840	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs258748	0.95[ASN][1000 genomes]
rs258750	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs258751	0.95[ASN][1000 genomes]
rs258752	0.80[ASN][1000 genomes]
rs258753	0.96[CEU][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs258813	0.87[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs258814	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2918415	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2918416	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2918417	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2918418	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2918419	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2963148	1.00[ASN][1000 genomes]
rs2963149	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2963150	1.00[ASN][1000 genomes]
rs2963151	1.00[JPT][hapmap]
rs2963153	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2963154	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs33380	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33381	1.00[ASN][1000 genomes]
rs33382	1.00[ASN][1000 genomes]
rs33389	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4128428	0.85[GIH][hapmap]
rs6188	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6194	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6196	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6198	0.85[GIH][hapmap]
rs6861962	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs712189	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs72801090	0.95[ASN][1000 genomes]
rs852975	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs852977	0.81[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs852978	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs852979	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs852982	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852984	1.00[ASN][1000 genomes]
rs853156	0.80[ASN][1000 genomes]
rs853157	1.00[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs853176	0.80[ASN][1000 genomes]
rs853179	0.83[ASN][1000 genomes]
rs853182	0.95[ASN][1000 genomes]
rs853184	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs860457	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs860458	0.95[ASN][1000 genomes]
rs864082	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs864355	0.83[ASN][1000 genomes]
rs865482	0.95[ASN][1000 genomes]
rs9324918	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[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	nsv1023976	chr5:142692062-142813664	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv969982	chr5:142757204-142762618	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:142725000-142764200	Weak transcription	Lung	lung
2	chr5:142739400-142763600	Weak transcription	Thymus	Thymus
3	chr5:142741600-142771600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr5:142742600-142762400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:142743200-142764200	Weak transcription	HepG2	liver
6	chr5:142744000-142762200	Weak transcription	K562	blood
7	chr5:142744600-142762400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr5:142745400-142764200	Weak transcription	Fetal Stomach	stomach
9	chr5:142746200-142760000	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr5:142747800-142762000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr5:142747800-142762200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:142748800-142761400	Weak transcription	Fetal Muscle Leg	muscle
13	chr5:142748800-142762200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr5:142749200-142761200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:142750400-142764200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr5:142751200-142764600	Weak transcription	Gastric	stomach
17	chr5:142752400-142764600	Weak transcription	Brain Angular Gyrus	brain
18	chr5:142752800-142762000	Weak transcription	Fetal Lung	lung
19	chr5:142752800-142763600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr5:142753200-142763000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr5:142753600-142763600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr5:142754400-142762800	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr5:142754600-142760000	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr5:142754600-142762000	Weak transcription	Primary B cells from cord blood	blood
25	chr5:142754800-142761200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr5:142754800-142762000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:142754800-142764000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr5:142755000-142761400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr5:142755400-142763400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr5:142756200-142762000	Weak transcription	Liver	Liver
31	chr5:142756400-142760800	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr5:142756600-142766400	Weak transcription	Pancreas	Pancrea
33	chr5:142756800-142763200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr5:142757000-142760400	Genic enhancers	Dnd41	blood
35	chr5:142757000-142762400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr5:142757000-142763800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr5:142757000-142763800	Weak transcription	Right Atrium	heart
38	chr5:142757000-142764200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr5:142757000-142764200	Weak transcription	Ovary	ovary
40	chr5:142757200-142762000	Weak transcription	Fetal Thymus	thymus
41	chr5:142757200-142763000	Weak transcription	HSMMtube	muscle
42	chr5:142757200-142763600	Weak transcription	Brain Hippocampus Middle	brain
43	chr5:142757200-142764200	Weak transcription	Aorta	Aorta
44	chr5:142757200-142764200	Weak transcription	Spleen	Spleen
45	chr5:142757400-142760000	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr5:142757400-142761800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr5:142757400-142762000	Weak transcription	Left Ventricle	heart
48	chr5:142757400-142762200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr5:142757400-142762200	Weak transcription	Fetal Heart	heart
50	chr5:142757400-142762400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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