Variant report

Variant	rs28667784
Chromosome Location	chr4:99229182-99229183
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 169 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:159)

rs_ID	r²[population]
rs10001086	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10001453	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10002767	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10003618	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10005811	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10006820	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10010135	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10012125	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10014034	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10014088	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10017792	0.93[EUR][1000 genomes]
rs10018670	0.86[ASN][1000 genomes]
rs10022047	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10022966	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10023500	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10025306	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10028275	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10028373	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10029454	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10030765	0.89[EUR][1000 genomes]
rs10032440	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10454790	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10470895	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10470952	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10516429	0.83[EUR][1000 genomes]
rs10516431	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12498437	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12498745	0.93[ASN][1000 genomes]
rs12499009	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12499530	0.93[ASN][1000 genomes]
rs12499799	0.83[EUR][1000 genomes]
rs12501974	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12502351	0.83[EUR][1000 genomes]
rs12503117	0.93[ASN][1000 genomes]
rs12503806	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12505246	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12507859	0.83[EUR][1000 genomes]
rs12508445	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12509125	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12509417	0.83[EUR][1000 genomes]
rs12509834	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12510055	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12510095	0.83[EUR][1000 genomes]
rs12510670	0.86[ASN][1000 genomes]
rs12512117	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12512920	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13353584	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1399242	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1453344	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1453345	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1533328	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1580065	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1580066	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17027330	0.86[ASN][1000 genomes]
rs17027331	0.86[ASN][1000 genomes]
rs17027339	0.86[ASN][1000 genomes]
rs17027386	0.93[ASN][1000 genomes]
rs17027412	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17027449	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17027452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17027454	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17027543	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17027564	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1913489	0.83[EUR][1000 genomes]
rs1913490	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2042653	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2042654	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2063745	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2081490	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2090118	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2194896	0.93[ASN][1000 genomes]
rs28367114	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28372185	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28409461	0.86[ASN][1000 genomes]
rs28411105	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28470922	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28536684	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28540371	0.86[ASN][1000 genomes]
rs28603037	0.86[ASN][1000 genomes]
rs28613236	0.86[ASN][1000 genomes]
rs28644420	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28656298	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28666485	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28703816	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28715883	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28862004	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34491917	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35484325	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3775538	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3822115	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3974886	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4321644	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4557264	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4593139	0.83[EUR][1000 genomes]
rs4699333	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4699334	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4699335	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4699336	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4699338	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4699341	0.83[EUR][1000 genomes]
rs4699342	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4699616	0.86[ASN][1000 genomes]
rs4699617	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4699622	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4699623	0.85[EUR][1000 genomes]
rs4699626	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4699627	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4699631	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4699632	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56376105	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56987276	0.83[EUR][1000 genomes]
rs58118567	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60613860	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61080824	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6532732	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6811171	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6811725	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6813960	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6814081	0.86[ASN][1000 genomes]
rs6814168	0.86[ASN][1000 genomes]
rs6820913	0.86[ASN][1000 genomes]
rs6821608	0.86[ASN][1000 genomes]
rs6822914	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6828936	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6831497	0.83[EUR][1000 genomes]
rs6831730	0.83[EUR][1000 genomes]
rs6833504	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6833596	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6834829	0.87[EUR][1000 genomes]
rs6835411	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6843874	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6846417	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72894301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72896317	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72896364	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72898390	0.86[ASN][1000 genomes]
rs72898391	0.86[ASN][1000 genomes]
rs7440164	0.83[EUR][1000 genomes]
rs7654497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7655147	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7663435	0.86[ASN][1000 genomes]
rs7664210	0.92[EUR][1000 genomes]
rs7673119	0.81[AMR][1000 genomes]
rs7676060	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7676285	0.94[EUR][1000 genomes]
rs7678942	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7683964	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7687685	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7692963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7695463	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs890207	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs919027	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs919028	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9990962	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9991874	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9992518	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9996568	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9997665	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9997666	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv1001570	chr4:98976239-99239838	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1004616	chr4:99085875-99308901	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2763801	chr4:99094892-99413853	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv879651	chr4:99105055-99441349	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv879652	chr4:99125659-99303633	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv528127	chr4:99146436-99229839	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv879653	chr4:99152631-99260423	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1004181	chr4:99208152-99529576	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99184000-99239600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr4:99184200-99242200	Weak transcription	A549	lung
3	chr4:99185400-99239400	Weak transcription	NHEK	skin
4	chr4:99206000-99234800	Weak transcription	Pancreas	Pancrea
5	chr4:99206200-99232800	Weak transcription	Gastric	stomach
6	chr4:99206200-99234000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:99206200-99239800	Weak transcription	Aorta	Aorta
8	chr4:99210200-99250800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr4:99212400-99239800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr4:99212400-99287800	Weak transcription	Thymus	Thymus
11	chr4:99213400-99229200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:99214200-99240800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:99215000-99235400	Weak transcription	HSMMtube	muscle
14	chr4:99215000-99235600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr4:99215000-99317000	Weak transcription	Left Ventricle	heart
16	chr4:99216800-99236000	Weak transcription	HUVEC	blood vessel
17	chr4:99216800-99236000	Weak transcription	NH-A	brain
18	chr4:99216800-99236000	Weak transcription	NHDF-Ad	bronchial
19	chr4:99216800-99239200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr4:99217000-99237400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr4:99217000-99239400	Weak transcription	HMEC	breast
22	chr4:99217600-99235800	Weak transcription	HSMM	muscle
23	chr4:99219000-99252000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr4:99219600-99236400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:99219600-99244600	Weak transcription	Fetal Thymus	thymus
26	chr4:99221400-99234800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:99223800-99234400	Weak transcription	Dnd41	blood
28	chr4:99223800-99288000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr4:99224400-99240000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:99224400-99247400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:99225200-99253400	Weak transcription	Fetal Lung	lung
32	chr4:99225400-99240600	Weak transcription	Primary B cells from cord blood	blood
33	chr4:99225600-99236000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:99226400-99232800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr4:99226400-99238800	Weak transcription	Fetal Intestine Small	intestine
36	chr4:99226600-99239200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr4:99227000-99243000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr4:99227200-99238000	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr4:99227400-99236400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:99227600-99234400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr4:99227800-99231400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr4:99227800-99236200	Weak transcription	Primary T cells from cord blood	blood
43	chr4:99229000-99229200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:99229000-99229200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:99229000-99232800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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