Variant report

Variant	rs7039105
Chromosome Location	chr9:21855096-21855097
allele	G/T
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	chr9:21854180-21856002	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr9:21854597-21855183	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr9:21854884-21855116	HCT-116	colon:	n/a	n/a
4	CEBPB	chr9:21854548-21855103	HCT-116	colon:	n/a	n/a
5	POLR2A	chr9:21854574-21855601	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
MTAP	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs4320630	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4478653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6475591	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7027989	0.82[JPT][hapmap]
rs7036197	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7039105	MTAP	cis	parietal	SCAN
rs7039105	MTAP	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21841400-21858800	Weak transcription	Colonic Mucosa	Colon
2	chr9:21841600-21858400	Weak transcription	Spleen	Spleen
3	chr9:21841800-21855400	Weak transcription	Gastric	stomach
4	chr9:21841800-21856200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr9:21841800-21856400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr9:21841800-21858600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr9:21841800-21864600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:21842000-21857800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr9:21842000-21858400	Weak transcription	Right Ventricle	heart
10	chr9:21846600-21869800	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr9:21847600-21871600	Strong transcription	Dnd41	blood
12	chr9:21848000-21869600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr9:21848200-21856200	Strong transcription	Primary T cells from cord blood	blood
14	chr9:21848800-21861400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr9:21848800-21866000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:21849000-21855400	Weak transcription	Lung	lung
17	chr9:21849000-21856200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr9:21849000-21858200	Weak transcription	Colon Smooth Muscle	Colon
19	chr9:21849000-21858400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:21849000-21859600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr9:21849000-21859600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr9:21849000-21861800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr9:21849000-21862200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr9:21849000-21864200	Weak transcription	Brain Germinal Matrix	brain
25	chr9:21849000-21865800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr9:21849000-21868200	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr9:21849000-21870000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr9:21849000-21870200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr9:21849200-21855200	Weak transcription	Brain Anterior Caudate	brain
30	chr9:21849200-21866200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr9:21849600-21864600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr9:21850000-21855400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr9:21850000-21859400	Weak transcription	Brain Angular Gyrus	brain
34	chr9:21850400-21855200	Weak transcription	Aorta	Aorta
35	chr9:21850400-21863800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:21851000-21855400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr9:21851400-21866800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr9:21852400-21855400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr9:21852400-21856800	Enhancers	Fetal Intestine Small	intestine
40	chr9:21852400-21857400	Enhancers	Stomach Mucosa	stomach
41	chr9:21852600-21866000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr9:21853000-21857600	Genic enhancers	HepG2	liver
43	chr9:21853200-21855200	Weak transcription	Small Intestine	intestine
44	chr9:21853600-21856400	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr9:21853600-21864600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr9:21853800-21862600	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr9:21853800-21866800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr9:21854000-21859800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
49	chr9:21854000-21862400	Strong transcription	Fetal Thymus	thymus
50	chr9:21854000-21864000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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