Variant report

Variant	rs28682280
Chromosome Location	chr15:57259356-57259357
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12101705	1.00[AMR][1000 genomes]
rs12102211	0.89[AFR][1000 genomes]
rs12903733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16977069	1.00[AMR][1000 genomes]
rs16977150	1.00[AMR][1000 genomes]
rs16977156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16977168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16977178	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16977180	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16977183	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16977196	1.00[AMR][1000 genomes]
rs16977206	1.00[AMR][1000 genomes]
rs16977215	1.00[AMR][1000 genomes]
rs16977236	1.00[AMR][1000 genomes]
rs2733189	1.00[AMR][1000 genomes]
rs28393473	0.83[AFR][1000 genomes]
rs28464293	0.89[AFR][1000 genomes]
rs28493156	0.89[AFR][1000 genomes]
rs28494971	1.00[AMR][1000 genomes]
rs28637784	1.00[AMR][1000 genomes]
rs28647446	1.00[AMR][1000 genomes]
rs28648947	1.00[AMR][1000 genomes]
rs28669321	1.00[AMR][1000 genomes]
rs28710916	1.00[AMR][1000 genomes]
rs28718703	1.00[AMR][1000 genomes]
rs28760390	1.00[AMR][1000 genomes]
rs28790102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28807215	1.00[AMR][1000 genomes]
rs3111100	1.00[AMR][1000 genomes]
rs57498481	1.00[AMR][1000 genomes]
rs57637767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59225036	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73427621	1.00[AMR][1000 genomes]
rs8030618	1.00[AMR][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	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv904250	chr15:57225766-57294085	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1052052	chr15:57232111-57344561	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv542394	chr15:57232111-57344561	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57227600-57260600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:57228200-57260600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:57251000-57260600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr15:57251000-57261000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:57251800-57260800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:57255000-57259800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr15:57256200-57260800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:57256200-57260800	Weak transcription	Stomach Mucosa	stomach
9	chr15:57256200-57263400	Weak transcription	Lung	lung
10	chr15:57256200-57264400	Weak transcription	NH-A	brain
11	chr15:57256200-57265200	Weak transcription	Fetal Brain Male	brain
12	chr15:57256200-57265800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr15:57256400-57260000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr15:57256400-57261400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr15:57256400-57263600	Weak transcription	Brain Germinal Matrix	brain
16	chr15:57256400-57264000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr15:57256400-57265200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr15:57256600-57260800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr15:57256800-57259600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr15:57256800-57259600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr15:57256800-57259600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:57256800-57259600	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:57256800-57259600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr15:57256800-57259600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr15:57256800-57259600	Weak transcription	Right Ventricle	heart
26	chr15:57256800-57259600	Weak transcription	Thymus	Thymus
27	chr15:57256800-57259600	Weak transcription	K562	blood
28	chr15:57256800-57259800	Weak transcription	Brain Angular Gyrus	brain
29	chr15:57256800-57259800	Weak transcription	Ovary	ovary
30	chr15:57256800-57260200	Weak transcription	Pancreas	Pancrea
31	chr15:57256800-57260200	Weak transcription	Psoas Muscle	Psoas
32	chr15:57256800-57260600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:57256800-57260600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:57256800-57260600	Weak transcription	Gastric	stomach
35	chr15:57256800-57260600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:57256800-57260600	Weak transcription	Dnd41	blood
37	chr15:57256800-57260600	Weak transcription	HMEC	breast
38	chr15:57256800-57260800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr15:57256800-57260800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr15:57256800-57260800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr15:57256800-57261000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr15:57256800-57263000	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr15:57256800-57263600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr15:57256800-57263600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:57256800-57264400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:57256800-57277200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr15:57257000-57259400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr15:57257000-57259800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr15:57257000-57260600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr15:57257000-57260600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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