Variant report

Variant	rs28483598
Chromosome Location	chr19:42874900-42874901
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10401224	1.00[EUR][1000 genomes]
rs10402438	1.00[EUR][1000 genomes]
rs10403856	1.00[AMR][1000 genomes]
rs10404650	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10406800	1.00[AMR][1000 genomes]
rs10406972	1.00[EUR][1000 genomes]
rs10407085	1.00[EUR][1000 genomes]
rs10407155	1.00[EUR][1000 genomes]
rs10407842	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10408258	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10408986	1.00[AMR][1000 genomes]
rs10409428	1.00[EUR][1000 genomes]
rs10409433	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10409939	1.00[EUR][1000 genomes]
rs10410129	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10410174	1.00[AMR][1000 genomes]
rs10410653	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10411498	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10411908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10413484	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10414056	0.81[AFR][1000 genomes]
rs10414695	1.00[AMR][1000 genomes]
rs10415759	1.00[AMR][1000 genomes]
rs10415999	1.00[EUR][1000 genomes]
rs10416535	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10417606	1.00[AMR][1000 genomes]
rs10418102	1.00[AMR][1000 genomes]
rs10418312	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10418988	1.00[AMR][1000 genomes]
rs10420327	1.00[AMR][1000 genomes]
rs10421026	0.84[AFR][1000 genomes]
rs10421331	1.00[AMR][1000 genomes]
rs10421409	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10421510	1.00[EUR][1000 genomes]
rs10421857	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10421902	1.00[AMR][1000 genomes]
rs10422301	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10422867	1.00[EUR][1000 genomes]
rs10423812	1.00[EUR][1000 genomes]
rs10423959	1.00[EUR][1000 genomes]
rs10423978	1.00[EUR][1000 genomes]
rs10424402	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10425003	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10425320	1.00[EUR][1000 genomes]
rs10425783	1.00[EUR][1000 genomes]
rs10426267	1.00[EUR][1000 genomes]
rs10426284	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11878207	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11878297	1.00[EUR][1000 genomes]
rs11879073	1.00[EUR][1000 genomes]
rs11879538	1.00[EUR][1000 genomes]
rs11880214	1.00[EUR][1000 genomes]
rs11880356	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11882107	1.00[EUR][1000 genomes]
rs11882801	1.00[EUR][1000 genomes]
rs12165130	1.00[EUR][1000 genomes]
rs13343322	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13343388	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13343719	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13343761	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13343834	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13343966	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13345986	0.81[AFR][1000 genomes]
rs13346831	1.00[AMR][1000 genomes]
rs13346837	1.00[EUR][1000 genomes]
rs13346879	1.00[AMR][1000 genomes]
rs2229614	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28402882	1.00[AMR][1000 genomes]
rs28463673	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28469564	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28474957	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28496975	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28532592	0.81[AFR][1000 genomes]
rs28657829	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28663042	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28675019	1.00[EUR][1000 genomes]
rs28675764	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28686771	1.00[AMR][1000 genomes]
rs28699037	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28711448	1.00[EUR][1000 genomes]
rs28715574	1.00[EUR][1000 genomes]
rs33919763	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35707383	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36089262	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41407146	1.00[AMR][1000 genomes]
rs59870753	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60950516	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6509012	0.81[AFR][1000 genomes]
rs7246232	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7248473	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7254853	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7255343	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7258727	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73552879	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73554520	1.00[EUR][1000 genomes]
rs73554531	1.00[EUR][1000 genomes]
rs73558432	1.00[AMR][1000 genomes]
rs73560411	1.00[AMR][1000 genomes]
rs8099885	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8109258	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9304602	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
5	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
6	nsv911785	chr19:42741124-42917545	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42830800-42879200	Weak transcription	Small Intestine	intestine
2	chr19:42830800-42884200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr19:42831600-42882600	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr19:42844800-42877400	Weak transcription	Stomach Mucosa	stomach
5	chr19:42862600-42878800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:42868400-42876200	Weak transcription	Lung	lung
7	chr19:42868400-42879200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr19:42868400-42881400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr19:42868400-42882400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr19:42868600-42878800	Weak transcription	Esophagus	oesophagus
11	chr19:42868600-42878800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr19:42868600-42879000	Weak transcription	Aorta	Aorta
13	chr19:42868600-42882600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr19:42868800-42878800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr19:42868800-42878800	Weak transcription	Gastric	stomach
16	chr19:42868800-42878800	Weak transcription	Thymus	Thymus
17	chr19:42868800-42878800	Weak transcription	Dnd41	blood
18	chr19:42868800-42880800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr19:42868800-42882000	Strong transcription	Fetal Stomach	stomach
20	chr19:42869000-42875200	Weak transcription	Brain Substantia Nigra	brain
21	chr19:42869000-42875600	Weak transcription	Right Ventricle	heart
22	chr19:42869000-42878200	Weak transcription	Liver	Liver
23	chr19:42869000-42878800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr19:42869000-42878800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr19:42869000-42883400	Weak transcription	Primary T cells from cord blood	blood
26	chr19:42869000-42884400	Weak transcription	Colonic Mucosa	Colon
27	chr19:42869200-42879000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr19:42869400-42878800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:42869600-42875200	Weak transcription	Pancreas	Pancrea
30	chr19:42869600-42880200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr19:42869600-42890800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr19:42869800-42875200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr19:42869800-42875400	Weak transcription	Adipose Nuclei	Adipose
34	chr19:42869800-42878800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr19:42870400-42876600	Strong transcription	Brain Germinal Matrix	brain
36	chr19:42870600-42876000	Weak transcription	Right Atrium	heart
37	chr19:42870800-42881400	Strong transcription	Brain Anterior Caudate	brain
38	chr19:42871000-42875000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr19:42871000-42878800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr19:42871400-42878800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr19:42871400-42890800	Weak transcription	Psoas Muscle	Psoas
42	chr19:42871800-42881400	Strong transcription	Fetal Brain Female	brain
43	chr19:42872000-42875000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr19:42872000-42875400	Weak transcription	Colon Smooth Muscle	Colon
45	chr19:42872000-42875600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr19:42872000-42878800	Weak transcription	Left Ventricle	heart
47	chr19:42872000-42884800	Weak transcription	A549	lung
48	chr19:42872200-42875800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:42872200-42876000	Enhancers	H1 Cell Line	embryonic stem cell
50	chr19:42872200-42876800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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