Variant report

Variant	rs28674880
Chromosome Location	chr15:43163312-43163313
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10518779	0.83[ASN][1000 genomes]
rs13329197	0.83[AMR][1000 genomes]
rs16957277	0.87[ASN][1000 genomes]
rs28392857	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28609797	0.90[ASN][1000 genomes]
rs28649962	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28858165	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182515	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8028785	0.83[ASN][1000 genomes]
rs9920202	0.95[ASN][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	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv977054	chr15:43015821-43171355	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1050128	chr15:43056145-43262736	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv542368	chr15:43056145-43262736	Flanking Active TSS Weak transcription Strong transcription Active TSS 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	7 gene(s)	inside rSNPs	diseases
5	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv904134	chr15:43097652-43357406	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv515876	chr15:43116906-43445305	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	esv3400306	chr15:43135709-43164903	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv904135	chr15:43143998-43392075	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	esv3490431	chr15:43148709-43190630	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv3490432	chr15:43148709-43190630	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43089800-43165200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr15:43094400-43163800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr15:43095000-43165000	Weak transcription	Spleen	Spleen
4	chr15:43103000-43165400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr15:43103400-43173200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:43114800-43172000	Weak transcription	Pancreas	Pancrea
7	chr15:43119600-43168200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr15:43119600-43172600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr15:43119800-43170200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr15:43125400-43173600	Weak transcription	Hela-S3	cervix
11	chr15:43131000-43165200	Weak transcription	Thymus	Thymus
12	chr15:43131600-43171800	Weak transcription	Brain Anterior Caudate	brain
13	chr15:43132000-43186800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr15:43132200-43166200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:43132400-43165400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr15:43132400-43172800	Weak transcription	Ovary	ovary
17	chr15:43132600-43171200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:43136600-43167200	Weak transcription	Dnd41	blood
19	chr15:43136800-43165200	Weak transcription	Brain Germinal Matrix	brain
20	chr15:43136800-43169200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr15:43136800-43169200	Weak transcription	Fetal Intestine Small	intestine
22	chr15:43136800-43182400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr15:43137000-43164000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr15:43140000-43164600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:43142400-43182400	Weak transcription	Lung	lung
26	chr15:43142600-43169400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr15:43142600-43170200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr15:43142800-43172000	Weak transcription	Fetal Intestine Large	intestine
29	chr15:43145400-43169200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr15:43151000-43169400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr15:43151600-43182400	Weak transcription	Aorta	Aorta
32	chr15:43151800-43163600	Weak transcription	Esophagus	oesophagus
33	chr15:43151800-43169200	Weak transcription	Fetal Muscle Leg	muscle
34	chr15:43151800-43173000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr15:43151800-43178600	Weak transcription	Placenta	Placenta
36	chr15:43152200-43167400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr15:43152200-43170000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr15:43154200-43174000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr15:43154600-43182400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:43155000-43182600	Weak transcription	Primary T cells from cord blood	blood
41	chr15:43156000-43165000	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr15:43156000-43171400	Weak transcription	Fetal Brain Male	brain
43	chr15:43156000-43172400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr15:43156000-43172800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr15:43156800-43172000	Weak transcription	Gastric	stomach
46	chr15:43157600-43171600	Weak transcription	Liver	Liver
47	chr15:43157800-43165800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:43158000-43165000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr15:43158000-43165400	Weak transcription	Adipose Nuclei	Adipose
50	chr15:43158000-43169400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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