Variant report

Variant	rs28364392
Chromosome Location	chr15:42677947-42677948
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42281641..42282425-chr15:42677780..42678339,2	K562	blood:
2	chr15:42429166..42430382-chr15:42677434..42678387,4	K562	blood:
3	chr15:42677853..42678408-chr15:42942399..42943222,2	K562	blood:

Variant related genes	Relation type
ENSG00000188089	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1044866	1.00[CHB][hapmap]
rs17592	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364364	1.00[CHB][hapmap]
rs28364389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364395	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364396	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364407	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364432	1.00[ASW][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs28364443	1.00[ASW][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364446	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364451	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364454	1.00[ASW][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364481	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364485	1.00[ASW][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364496	1.00[ASW][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364534	1.00[ASW][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs28364542	1.00[CHB][hapmap]
rs7169432	1.00[AMR][1000 genomes]
rs7176832	1.00[ASW][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7182306	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8028539	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking 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 miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv904133	chr15:42528982-42681057	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv832986	chr15:42587825-42753664	Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv832987	chr15:42627447-42792348	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv932995	chr15:42640015-42704121	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv3334708	chr15:42664344-42827738	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42646000-42678600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:42647800-42678200	Weak transcription	Ovary	ovary
3	chr15:42652800-42684400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr15:42653200-42691600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr15:42656000-42678800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr15:42656800-42693400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:42656800-42697800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:42657200-42678800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr15:42663000-42691400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:42663200-42678400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr15:42672400-42688800	Weak transcription	Esophagus	oesophagus
12	chr15:42673400-42691800	Weak transcription	Primary T cells from cord blood	blood
13	chr15:42673800-42678000	Weak transcription	Fetal Intestine Small	intestine
14	chr15:42673800-42678200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:42674000-42694400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr15:42674600-42678200	Weak transcription	Aorta	Aorta
17	chr15:42674600-42682600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr15:42674600-42684400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr15:42674800-42678400	Weak transcription	Brain Anterior Caudate	brain
20	chr15:42675200-42683600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr15:42675200-42684800	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr15:42675200-42702800	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:42675600-42691600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr15:42675800-42678800	Weak transcription	Brain Angular Gyrus	brain
25	chr15:42676200-42678000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr15:42676200-42682400	Strong transcription	Liver	Liver
27	chr15:42676400-42678000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
28	chr15:42676400-42678400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:42676400-42679000	Strong transcription	Primary B cells from peripheral blood	blood
30	chr15:42676400-42679200	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr15:42676400-42679600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr15:42676400-42680600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr15:42676600-42678200	Enhancers	H9 Cell Line	embryonic stem cell
34	chr15:42676600-42678400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
35	chr15:42676600-42678400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
36	chr15:42676600-42678600	Enhancers	H1 Cell Line	embryonic stem cell
37	chr15:42676600-42679200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:42676600-42679800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr15:42676600-42680000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr15:42676600-42680200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:42676800-42678200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr15:42676800-42678200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr15:42676800-42679000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr15:42676800-42679200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr15:42676800-42679600	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr15:42676800-42680200	Genic enhancers	Fetal Muscle Leg	muscle
47	chr15:42676800-42680400	Strong transcription	Primary B cells from cord blood	blood
48	chr15:42676800-42693200	Weak transcription	Fetal Stomach	stomach
49	chr15:42677000-42678000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr15:42677000-42693400	Weak transcription	GM12878-XiMat	blood

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