Variant report

Variant	rs8038978
Chromosome Location	chr15:42560820-42560821
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:42560810-42560878	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42559733..42563310-chr15:42678634..42681534,3	K562	blood:

Variant related genes	Relation type
GANC	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11070368	0.87[AFR][1000 genomes]
rs11858453	0.87[AFR][1000 genomes]
rs12913755	0.87[AFR][1000 genomes]
rs2412677	0.87[AFR][1000 genomes]
rs2412679	0.81[EUR][1000 genomes]
rs2412680	0.82[AMR][1000 genomes]
rs2412681	0.87[AFR][1000 genomes]
rs2899043	0.93[AFR][1000 genomes]
rs6493028	0.87[AFR][1000 genomes]
rs6493029	0.87[AFR][1000 genomes]
rs8040580	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv1807328	chr15:42525300-42573278	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
7	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

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42500800-42563200	Weak transcription	Stomach Mucosa	stomach
2	chr15:42519400-42562800	Weak transcription	Fetal Heart	heart
3	chr15:42520200-42561000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:42542800-42561600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:42543400-42561200	Strong transcription	Liver	Liver
6	chr15:42543600-42561000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:42543800-42561600	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr15:42544200-42561000	Strong transcription	Rectal Mucosa Donor 31	rectum
9	chr15:42544200-42561200	Strong transcription	Primary B cells from peripheral blood	blood
10	chr15:42544200-42561200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr15:42544200-42561800	Strong transcription	Osteobl	bone
12	chr15:42544400-42561200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr15:42544400-42561200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:42544600-42561600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:42545000-42561400	Strong transcription	HSMM	muscle
16	chr15:42545600-42563400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr15:42545800-42561400	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr15:42546000-42564600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr15:42546200-42564600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr15:42546400-42561000	Strong transcription	Dnd41	blood
21	chr15:42546600-42561600	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr15:42547000-42564200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr15:42547600-42561200	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr15:42547600-42563400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:42548600-42561200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr15:42548800-42561200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:42548800-42561200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr15:42548800-42561400	Strong transcription	Hela-S3	cervix
29	chr15:42549600-42561200	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr15:42549600-42564400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr15:42550000-42561200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr15:42551000-42561400	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:42551000-42563400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:42551800-42561400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:42551800-42564600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr15:42552400-42563400	Weak transcription	Brain Angular Gyrus	brain
37	chr15:42552600-42564600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:42552600-42565000	Weak transcription	Gastric	stomach
39	chr15:42552600-42565200	Weak transcription	Spleen	Spleen
40	chr15:42552800-42564600	Weak transcription	Aorta	Aorta
41	chr15:42552800-42564600	Weak transcription	Esophagus	oesophagus
42	chr15:42552800-42564600	Weak transcription	Right Ventricle	heart
43	chr15:42555800-42562400	Weak transcription	Pancreas	Pancrea
44	chr15:42556000-42562400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:42556000-42562600	Weak transcription	Ovary	ovary
46	chr15:42556000-42563000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr15:42556000-42563600	Weak transcription	Fetal Stomach	stomach
48	chr15:42556000-42564600	Weak transcription	Lung	lung
49	chr15:42556000-42565000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr15:42556200-42561400	Strong transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links