Variant report

Variant	rs2379996
Chromosome Location	chr15:83488773-83488774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83487140..83490123-chr15:83495534..83497188,2	K562	blood:
2	chr15:83477554..83479674-chr15:83486165..83489315,3	MCF-7	breast:
3	chr15:83477828..83481866-chr15:83483118..83489176,7	K562	blood:
4	chr15:83481406..83484295-chr15:83488515..83491028,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156232	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11259948	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11259949	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11259952	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1271044	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12902970	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12903411	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12907913	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1971555	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2890314	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66851469	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8025432	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8041231	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv977747	chr15:83479370-83496161	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
5	nsv9288	chr15:83479484-83496828	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2379996	WHAMM	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83479600-83504200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:83479800-83504000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:83480000-83497000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:83480000-83501600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:83480200-83489000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr15:83480400-83493600	Weak transcription	Brain Germinal Matrix	brain
7	chr15:83480400-83500600	Weak transcription	Stomach Mucosa	stomach
8	chr15:83480400-83507000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:83481000-83499800	Weak transcription	Fetal Heart	heart
10	chr15:83481200-83507200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr15:83481400-83489200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:83481400-83489600	Strong transcription	Osteobl	bone
13	chr15:83481400-83490800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr15:83481400-83492000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr15:83481400-83500800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:83481400-83507000	Strong transcription	Placenta	Placenta
17	chr15:83481600-83491800	Weak transcription	Small Intestine	intestine
18	chr15:83481600-83492200	Weak transcription	Pancreas	Pancrea
19	chr15:83481600-83500800	Strong transcription	Fetal Thymus	thymus
20	chr15:83481600-83507000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr15:83481800-83488800	Strong transcription	Fetal Muscle Trunk	muscle
22	chr15:83481800-83488800	Strong transcription	Fetal Muscle Leg	muscle
23	chr15:83481800-83489400	Strong transcription	HSMMtube	muscle
24	chr15:83481800-83489600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:83481800-83490200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr15:83481800-83492600	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr15:83481800-83496400	Strong transcription	Liver	Liver
28	chr15:83481800-83499400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:83481800-83500000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr15:83481800-83506200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr15:83481800-83507000	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr15:83481800-83507600	Strong transcription	Adipose Nuclei	Adipose
33	chr15:83482000-83489200	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr15:83482000-83489400	Strong transcription	A549	lung
35	chr15:83482000-83489800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:83482000-83490400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr15:83482000-83490400	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr15:83482000-83492600	Strong transcription	Dnd41	blood
39	chr15:83482000-83500000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr15:83482000-83500200	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr15:83482000-83506800	Strong transcription	Fetal Intestine Large	intestine
42	chr15:83482000-83507000	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr15:83482200-83500200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr15:83482200-83507000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr15:83482400-83489200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:83482400-83489200	Strong transcription	Brain Anterior Caudate	brain
47	chr15:83482400-83490000	Strong transcription	HSMM	muscle
48	chr15:83482400-83495200	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr15:83482400-83496600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr15:83482600-83489000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links