Variant report

Variant	rs5024581
Chromosome Location	chr4:26780582-26780583
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	chr4:26779353..26784175-chr4:26785525..26789077,5	MCF-7	breast:
2	chr4:26778248..26781151-chr4:26791403..26794152,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBC1D19-2	chr4:26780029-26786640	NONHSAT095883

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10939134	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs10939135	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1129230	0.85[CEU][hapmap];0.95[GIH][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs1135204	0.84[EUR][1000 genomes]
rs11721891	0.89[CEU][hapmap];0.95[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs11724595	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11726910	0.89[ASN][1000 genomes]
rs11733702	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs11734761	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11931159	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs11937465	0.82[EUR][1000 genomes]
rs11942145	0.84[CEU][hapmap]
rs11944010	0.80[EUR][1000 genomes]
rs12498454	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12504472	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12505249	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs12505393	0.88[ASN][1000 genomes]
rs12507314	0.92[CEU][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12510371	0.91[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs12510995	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs12640312	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs12644574	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12647180	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12650361	0.85[CEU][hapmap];0.95[GIH][hapmap];0.83[TSI][hapmap]
rs13111381	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13112222	0.97[EUR][1000 genomes]
rs13121378	0.88[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap]
rs13123511	0.84[EUR][1000 genomes]
rs13125612	0.89[CEU][hapmap];0.95[GIH][hapmap];0.83[TSI][hapmap]
rs13131355	0.81[EUR][1000 genomes]
rs13138699	1.00[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs13138712	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs13146364	0.88[CEU][hapmap]
rs13146615	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs13151477	0.84[EUR][1000 genomes]
rs1565303	0.89[CEU][hapmap]
rs1619573	0.89[CEU][hapmap];0.93[GIH][hapmap];0.83[TSI][hapmap]
rs1641562	0.82[CEU][hapmap]
rs1861470	0.89[CEU][hapmap]
rs2111006	1.00[YRI][hapmap]
rs2309413	0.85[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs260948	0.85[CEU][hapmap]
rs260950	0.85[CEU][hapmap];0.95[GIH][hapmap];0.83[TSI][hapmap]
rs260958	0.85[CEU][hapmap];0.93[GIH][hapmap];0.83[TSI][hapmap]
rs260959	0.85[CEU][hapmap]
rs34010107	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34241157	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34837351	0.84[EUR][1000 genomes]
rs35124296	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35588742	0.97[EUR][1000 genomes]
rs35654367	0.82[EUR][1000 genomes]
rs4234981	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4321621	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4355378	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4437235	0.88[CEU][hapmap];0.95[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs4527463	0.88[CEU][hapmap];0.95[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs4588446	0.93[GIH][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs4590010	0.89[CEU][hapmap];0.95[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs4602486	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4692549	0.81[CEU][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs4692551	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55767426	0.98[EUR][1000 genomes]
rs56150091	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58565506	0.81[EUR][1000 genomes]
rs60503601	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60915838	0.81[EUR][1000 genomes]
rs61690082	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62299027	0.83[EUR][1000 genomes]
rs62300967	0.84[EUR][1000 genomes]
rs62300968	0.84[EUR][1000 genomes]
rs62412678	0.81[EUR][1000 genomes]
rs6448458	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs6821370	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs6858652	0.85[CEU][hapmap];0.95[GIH][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs7657453	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7658999	0.82[CEU][hapmap];0.95[GIH][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs7672267	0.82[EUR][1000 genomes]
rs7683324	0.89[CEU][hapmap]
rs7687087	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs7689475	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9790514	0.81[EUR][1000 genomes]
rs9790776	0.81[EUR][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	nsv470021	chr4:26721578-27067027	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1005550	chr4:26778410-26824285	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26719400-26780800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:26723400-26781000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:26746400-26789600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:26748200-26789000	Weak transcription	Gastric	stomach
5	chr4:26749400-26781000	Weak transcription	NHDF-Ad	bronchial
6	chr4:26749800-26789200	Weak transcription	Fetal Kidney	kidney
7	chr4:26750600-26781000	Weak transcription	Lung	lung
8	chr4:26754400-26781800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:26755600-26788600	Weak transcription	NHLF	lung
10	chr4:26757600-26789000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr4:26761400-26788800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr4:26768000-26789200	Weak transcription	HSMMtube	muscle
13	chr4:26771400-26789400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr4:26774200-26789000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:26774400-26783800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:26774400-26787600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr4:26774400-26789200	Weak transcription	Pancreas	Pancrea
18	chr4:26774800-26781000	Weak transcription	Primary T cells from cord blood	blood
19	chr4:26775800-26780800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:26775800-26780800	Weak transcription	Fetal Stomach	stomach
21	chr4:26775800-26781000	Weak transcription	Left Ventricle	heart
22	chr4:26775800-26782000	Weak transcription	Thymus	Thymus
23	chr4:26776000-26780600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:26776000-26780800	Weak transcription	Right Ventricle	heart
25	chr4:26776000-26783600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr4:26776000-26783800	Weak transcription	Ovary	ovary
27	chr4:26776000-26789000	Weak transcription	Fetal Thymus	thymus
28	chr4:26776000-26789000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:26776000-26789400	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr4:26776000-26789600	Weak transcription	Colon Smooth Muscle	Colon
31	chr4:26776000-26790000	Weak transcription	Brain Germinal Matrix	brain
32	chr4:26776200-26780800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:26776200-26781000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:26776200-26781000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:26776200-26781800	Weak transcription	Primary B cells from cord blood	blood
36	chr4:26776200-26783800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr4:26776200-26785200	Weak transcription	Dnd41	blood
38	chr4:26776200-26789200	Weak transcription	Fetal Lung	lung
39	chr4:26776200-26789400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:26776200-26789400	Weak transcription	Fetal Intestine Large	intestine
41	chr4:26776200-26789400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr4:26776400-26782000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:26776400-26782000	Weak transcription	Adipose Nuclei	Adipose
44	chr4:26776600-26780600	Weak transcription	Fetal Muscle Leg	muscle
45	chr4:26776800-26781000	Weak transcription	Osteobl	bone
46	chr4:26776800-26781200	Weak transcription	NH-A	brain
47	chr4:26777000-26789200	Weak transcription	Psoas Muscle	Psoas
48	chr4:26777200-26780800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr4:26777200-26784000	Weak transcription	Aorta	Aorta
50	chr4:26777400-26782200	Weak transcription	Primary hematopoietic stem cells	blood

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