Variant report

Variant	rs28828686
Chromosome Location	chr19:20299876-20299877
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10402115	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10402155	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10402722	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10404469	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10404767	1.00[AMR][1000 genomes]
rs10405110	1.00[AMR][1000 genomes]
rs10406552	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10406926	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408168	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10410951	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10412006	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10412042	1.00[AMR][1000 genomes]
rs10413166	1.00[AMR][1000 genomes]
rs10414005	1.00[AMR][1000 genomes]
rs10414093	1.00[AMR][1000 genomes]
rs10414627	1.00[AMR][1000 genomes]
rs10416696	1.00[AMR][1000 genomes]
rs10417651	1.00[AMR][1000 genomes]
rs10419576	1.00[AMR][1000 genomes]
rs10420381	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10420815	1.00[AMR][1000 genomes]
rs10421160	1.00[AMR][1000 genomes]
rs10421320	1.00[AMR][1000 genomes]
rs10422287	1.00[AMR][1000 genomes]
rs10424049	1.00[AMR][1000 genomes]
rs10424101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10424275	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10427104	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13343888	1.00[AMR][1000 genomes]
rs13344384	1.00[AMR][1000 genomes]
rs13344637	1.00[AFR][1000 genomes]
rs13345082	1.00[AMR][1000 genomes]
rs2017452	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28402094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28447348	1.00[AMR][1000 genomes]
rs28507750	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28514435	1.00[AMR][1000 genomes]
rs28526012	1.00[AMR][1000 genomes]
rs28567705	1.00[AMR][1000 genomes]
rs28690849	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28767893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59440664	1.00[AMR][1000 genomes]
rs9917066	1.00[AMR][1000 genomes]
rs9967629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519535	chr19:19871250-20595412	Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
2	esv3319016	chr19:19917475-20819154	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
3	esv3319017	chr19:19917475-20819154	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	nsv1061846	chr19:19946927-20595412	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	esv3390957	chr19:19965887-20819154	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
6	nsv869122	chr19:19969851-20595412	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
7	nsv1059158	chr19:19973489-20576161	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
8	nsv870354	chr19:20043821-20576175	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
9	nsv1066004	chr19:20053658-20592867	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
10	nsv543932	chr19:20053658-20592867	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
11	nsv1066564	chr19:20056348-20595412	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
12	nsv1066375	chr19:20061084-20574512	Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
13	nsv543934	chr19:20061084-20574512	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
14	nsv1057309	chr19:20072886-20595412	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
15	nsv578801	chr19:20084681-20595412	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
16	nsv1055694	chr19:20088866-20595412	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
17	nsv578802	chr19:20091702-20595412	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
18	nsv1064400	chr19:20101052-20595412	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
19	nsv911325	chr19:20151257-21071548	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
20	nsv1066014	chr19:20165112-20595412	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 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	chr19:20278800-20301200	Weak transcription	Aorta	Aorta
2	chr19:20278800-20311400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:20279000-20300800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr19:20279200-20301000	Weak transcription	NH-A	brain
5	chr19:20279200-20303400	Weak transcription	Brain Substantia Nigra	brain
6	chr19:20279200-20303400	Weak transcription	NHLF	lung
7	chr19:20279200-20306000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr19:20279200-20306600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr19:20279200-20308000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr19:20279200-20308400	Weak transcription	Colon Smooth Muscle	Colon
11	chr19:20280000-20315200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:20280200-20301200	Weak transcription	Gastric	stomach
13	chr19:20283000-20301200	Weak transcription	Thymus	Thymus
14	chr19:20283200-20308600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr19:20286400-20301200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr19:20287200-20301600	Weak transcription	Colonic Mucosa	Colon
17	chr19:20287200-20309400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr19:20288200-20307000	Weak transcription	Brain Hippocampus Middle	brain
19	chr19:20288600-20301200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr19:20288600-20301200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:20290800-20307200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr19:20291000-20308200	Weak transcription	Brain Anterior Caudate	brain
23	chr19:20292000-20301000	Weak transcription	Fetal Brain Male	brain
24	chr19:20293600-20301200	Weak transcription	Fetal Kidney	kidney
25	chr19:20294600-20307400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr19:20295200-20300800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr19:20295400-20300200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr19:20295400-20302200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
29	chr19:20295400-20310600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr19:20295400-20310800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr19:20295400-20316800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:20295600-20300200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:20295600-20300400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:20295600-20308200	Weak transcription	HSMMtube	muscle
35	chr19:20296200-20300200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr19:20296400-20300600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr19:20296600-20304200	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr19:20296800-20300000	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr19:20296800-20300200	Strong transcription	Primary B cells from peripheral blood	blood
40	chr19:20296800-20302200	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr19:20296800-20302200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr19:20296800-20302800	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr19:20296800-20303400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:20297000-20300000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr19:20297000-20302000	Strong transcription	NHDF-Ad	bronchial
46	chr19:20297000-20304000	Strong transcription	Osteobl	bone
47	chr19:20297200-20304400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr19:20297400-20301000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr19:20298200-20302200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
50	chr19:20298200-20303800	Strong transcription	Fetal Lung	lung

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