Variant report

Variant	rs28407079
Chromosome Location	chr15:55682936-55682937
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs28417106	1.00[AMR][1000 genomes]
rs28445247	1.00[AMR][1000 genomes]
rs55904532	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56368121	0.80[AFR][1000 genomes]
rs56849426	1.00[AMR][1000 genomes]
rs58851760	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59652532	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59887243	1.00[AMR][1000 genomes]
rs60146363	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61019518	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61044972	0.85[AMR][1000 genomes]
rs7177224	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406933	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406996	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408819	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408848	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408869	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413697	0.85[AMR][1000 genomes]
rs73415503	1.00[AMR][1000 genomes]
rs74015569	1.00[AMR][1000 genomes]
rs74015592	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1051046	chr15:55529291-55821973	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1036173	chr15:55547689-55812194	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv542391	chr15:55547689-55812194	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active 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 miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv569523	chr15:55555602-55836704	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv1040917	chr15:55562940-55943942	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv531054	chr15:55571230-55914205	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv904243	chr15:55627528-55734158	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer 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 miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv520799	chr15:55645661-55760522	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv1041635	chr15:55658171-55943942	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55611800-55699400	Weak transcription	Colonic Mucosa	Colon
2	chr15:55630000-55695000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:55630800-55683600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr15:55637000-55699600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr15:55647800-55695400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr15:55649800-55695800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr15:55666200-55684000	Weak transcription	HUVEC	blood vessel
8	chr15:55667600-55687000	Weak transcription	Pancreas	Pancrea
9	chr15:55668200-55699800	Weak transcription	Spleen	Spleen
10	chr15:55669400-55687200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:55669400-55690400	Weak transcription	Fetal Heart	heart
12	chr15:55670200-55695000	Weak transcription	Colon Smooth Muscle	Colon
13	chr15:55670800-55687000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr15:55671800-55690400	Weak transcription	Brain Angular Gyrus	brain
15	chr15:55671800-55695800	Weak transcription	HSMMtube	muscle
16	chr15:55672000-55687000	Weak transcription	Small Intestine	intestine
17	chr15:55672200-55696000	Weak transcription	Brain Substantia Nigra	brain
18	chr15:55676000-55687000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr15:55676000-55695000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr15:55676000-55699400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr15:55676200-55683200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr15:55676200-55686600	Weak transcription	K562	blood
23	chr15:55676200-55695200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:55676200-55695800	Weak transcription	Brain Hippocampus Middle	brain
25	chr15:55676400-55683400	Weak transcription	Brain Anterior Caudate	brain
26	chr15:55676400-55683800	Weak transcription	Dnd41	blood
27	chr15:55676400-55697200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:55676400-55699400	Weak transcription	Right Ventricle	heart
29	chr15:55676800-55686200	Weak transcription	Left Ventricle	heart
30	chr15:55676800-55686400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr15:55676800-55688600	Weak transcription	Aorta	Aorta
32	chr15:55676800-55695800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr15:55676800-55697600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:55677000-55686400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr15:55677000-55695600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr15:55677200-55685400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr15:55678200-55684400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr15:55678200-55699400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr15:55679400-55696800	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr15:55679600-55689600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr15:55679600-55694400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr15:55679600-55695000	Weak transcription	Fetal Intestine Large	intestine
43	chr15:55679800-55687000	Weak transcription	Fetal Brain Female	brain
44	chr15:55681000-55683000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:55681000-55686600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr15:55681000-55688600	Weak transcription	Adipose Nuclei	Adipose
47	chr15:55681000-55695000	Weak transcription	Primary B cells from peripheral blood	blood
48	chr15:55681000-55695800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr15:55681000-55697400	Weak transcription	Gastric	stomach
50	chr15:55681000-55699200	Weak transcription	Lung	lung

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