Variant report

Variant	rs2027484
Chromosome Location	chr9:21866500-21866501
allele	A/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	chr9:21866394-21866854	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000265194	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10117550	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10118406	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10965174	0.83[CEU][hapmap]
rs1134871	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11526324	0.83[CEU][hapmap]
rs11531716	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12553901	0.83[CEU][hapmap]
rs1418072	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs15735	0.81[AMR][1000 genomes]
rs3928893	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4352938	0.83[CEU][hapmap]
rs4593639	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4607704	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4607709	0.82[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4977569	0.83[CEU][hapmap]
rs4977737	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4977738	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4977739	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6475592	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7028211	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7047648	0.82[GIH][hapmap]
rs756641	0.83[CEU][hapmap]
rs7865071	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv892745	chr9:21857244-22006273	Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2027484	MTAP	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21846600-21869800	Strong transcription	HUES48 Cell Line	embryonic stem cell
2	chr9:21847600-21871600	Strong transcription	Dnd41	blood
3	chr9:21848000-21869600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr9:21849000-21868200	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr9:21849000-21870000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr9:21849000-21870200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:21851400-21866800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr9:21853800-21866800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr9:21854200-21870200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr9:21854400-21869800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr9:21854600-21867000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:21855400-21873000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr9:21855600-21879800	Weak transcription	Small Intestine	intestine
14	chr9:21855800-21868600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr9:21855800-21870600	Strong transcription	HMEC	breast
16	chr9:21856600-21871200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr9:21857000-21871200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr9:21857400-21883800	Weak transcription	Pancreas	Pancrea
19	chr9:21859000-21892000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr9:21860200-21879800	Weak transcription	Right Ventricle	heart
21	chr9:21860400-21867200	Weak transcription	Brain Angular Gyrus	brain
22	chr9:21860400-21867200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr9:21860400-21868600	Weak transcription	Thymus	Thymus
24	chr9:21862200-21886800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr9:21862400-21874200	Weak transcription	Fetal Heart	heart
26	chr9:21863200-21880800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr9:21863800-21867000	Strong transcription	NHEK	skin
28	chr9:21863800-21869800	Strong transcription	NH-A	brain
29	chr9:21863800-21870600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:21864200-21866600	Strong transcription	Hela-S3	cervix
31	chr9:21864200-21868400	Weak transcription	NHDF-Ad	bronchial
32	chr9:21864200-21870000	Weak transcription	HUVEC	blood vessel
33	chr9:21864200-21870200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr9:21864200-21872000	Weak transcription	Stomach Mucosa	stomach
35	chr9:21864400-21868000	Strong transcription	Fetal Kidney	kidney
36	chr9:21864400-21871000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr9:21864400-21872600	Weak transcription	Fetal Intestine Small	intestine
38	chr9:21864600-21866800	Strong transcription	HepG2	liver
39	chr9:21864600-21867600	Weak transcription	Fetal Brain Male	brain
40	chr9:21864800-21868800	Weak transcription	Aorta	Aorta
41	chr9:21864800-21868800	Weak transcription	Lung	lung
42	chr9:21864800-21869400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr9:21864800-21870200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr9:21864800-21875000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:21864800-21879400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr9:21865000-21869600	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr9:21865000-21869600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr9:21865000-21870200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:21865000-21872200	Weak transcription	Esophagus	oesophagus
50	chr9:21865000-21873400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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