Variant report

Variant	rs28676999
Chromosome Location	chr15:40569884-40569885
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40569275..40572340-chr15:40598555..40600997,3	K562	blood:
2	chr15:40567372..40572340-chr15:40598668..40601169,4	K562	blood:
3	chr15:40568927..40571070-chr15:40580800..40583678,2	K562	blood:
4	chr15:40567195..40571331-chr15:40615416..40618233,4	K562	blood:
5	chr15:40568122..40570850-chr15:40588216..40591112,2	K562	blood:
6	chr15:40569115..40573106-chr15:40573581..40578796,5	K562	blood:
7	chr15:40564122..40566181-chr15:40568293..40570201,2	K562	blood:

Variant related genes	Relation type
ENSG00000230778	Chromatin interaction
ENSG00000137843	Chromatin interaction
ENSG00000137841	Chromatin interaction
ENSG00000259330	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2305646	0.81[ASN][1000 genomes]
rs55927878	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs56203022	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs56205728	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56282503	0.90[EUR][1000 genomes];0.82[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	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv904095	chr15:40525430-40591570	Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv471240	chr15:40528155-40595627	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv904096	chr15:40550149-40604777	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv904097	chr15:40555065-40595627	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv517541	chr15:40557268-40595627	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	esv1850798	chr15:40560607-40622191	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv904098	chr15:40564576-40586537	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv457118	chr15:40565705-40606484	Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv569227	chr15:40565705-40606484	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40546000-40571800	Weak transcription	Right Ventricle	heart
2	chr15:40551400-40571000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr15:40553800-40570400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr15:40557200-40571800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:40559000-40570000	Weak transcription	Brain Anterior Caudate	brain
6	chr15:40559200-40570000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr15:40559400-40570200	Weak transcription	Brain Angular Gyrus	brain
8	chr15:40559400-40571600	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:40559600-40570000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:40559600-40570400	Strong transcription	Esophagus	oesophagus
11	chr15:40559600-40571800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:40560800-40571800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:40565600-40571800	Weak transcription	Right Atrium	heart
14	chr15:40566200-40570000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:40566400-40571800	Weak transcription	Gastric	stomach
16	chr15:40567000-40570600	Weak transcription	Fetal Intestine Large	intestine
17	chr15:40567000-40571800	Weak transcription	HMEC	breast
18	chr15:40567200-40572000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr15:40567400-40570200	Weak transcription	Stomach Mucosa	stomach
20	chr15:40567400-40571000	Weak transcription	Fetal Heart	heart
21	chr15:40567600-40570000	Strong transcription	Fetal Intestine Small	intestine
22	chr15:40568000-40573400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:40568400-40570000	Weak transcription	Lung	lung
24	chr15:40568800-40570200	Enhancers	GM12878-XiMat	blood
25	chr15:40568800-40570400	Enhancers	Spleen	Spleen
26	chr15:40569000-40570000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr15:40569000-40570200	Bivalent Enhancer	Dnd41	blood
28	chr15:40569000-40570400	Bivalent Enhancer	Fetal Thymus	thymus
29	chr15:40569000-40573800	Weak transcription	Pancreas	Pancrea
30	chr15:40569200-40570000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr15:40569200-40570200	Enhancers	Primary B cells from cord blood	blood
32	chr15:40569200-40570600	Bivalent Enhancer	Adipose Nuclei	Adipose
33	chr15:40569200-40571400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr15:40569200-40571400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr15:40569200-40572000	Enhancers	Primary hematopoietic stem cells	blood
36	chr15:40569400-40570200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr15:40569400-40571800	Weak transcription	NHEK	skin
38	chr15:40569400-40572800	Bivalent Enhancer	Fetal Muscle Leg	muscle
39	chr15:40569600-40570000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
40	chr15:40569600-40570000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:40569600-40570000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:40569600-40570200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:40569600-40570200	Bivalent/Poised TSS	Osteobl	bone
44	chr15:40569600-40570400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
45	chr15:40569600-40570400	Weak transcription	Placenta	Placenta
46	chr15:40569600-40570600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
47	chr15:40569800-40570000	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr15:40569800-40570000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
49	chr15:40569800-40570000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
50	chr15:40569800-40570000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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