Variant report

Variant	rs2390538
Chromosome Location	chr7:21542891-21542892
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1011167	0.83[GIH][hapmap]
rs10268512	0.83[EUR][1000 genomes]
rs1771	0.80[EUR][1000 genomes]
rs2107449	0.82[LWK][hapmap]
rs28516066	0.81[AMR][1000 genomes]
rs3807642	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6461571	0.81[AMR][1000 genomes]
rs6966442	0.81[GIH][hapmap]
rs9648275	0.84[EUR][1000 genomes]
rs9791769	0.91[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027302	chr7:21391598-21727016	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv538800	chr7:21391598-21727016	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1028434	chr7:21468437-21636671	ZNF genes & repeats Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1023655	chr7:21486485-21727016	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv538801	chr7:21486485-21727016	ZNF genes & repeats Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv830921	chr7:21489100-21688016	Strong transcription ZNF genes & repeats Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2390538	MAGEA8	trans	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21487400-21557000	Weak transcription	Aorta	Aorta
2	chr7:21492200-21545200	Weak transcription	Small Intestine	intestine
3	chr7:21498600-21543600	Weak transcription	Pancreas	Pancrea
4	chr7:21500000-21552800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr7:21516200-21556400	Weak transcription	Brain Substantia Nigra	brain
6	chr7:21517000-21556000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr7:21520800-21552800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr7:21521200-21552600	Weak transcription	Brain Angular Gyrus	brain
9	chr7:21531400-21544400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr7:21533200-21547600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr7:21533400-21550400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr7:21533600-21549800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr7:21536600-21543400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr7:21536600-21549400	Weak transcription	Left Ventricle	heart
15	chr7:21536600-21550000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr7:21536600-21550600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr7:21536600-21557000	Weak transcription	Psoas Muscle	Psoas
18	chr7:21536800-21544000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr7:21536800-21550800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr7:21536800-21550800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr7:21536800-21552800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr7:21537000-21543000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr7:21537000-21547800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr7:21537400-21549000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr7:21538800-21555000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr7:21539200-21552600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr7:21539600-21554800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr7:21539600-21555800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr7:21539800-21551600	Strong transcription	Primary B cells from cord blood	blood
30	chr7:21540000-21543000	Strong transcription	Primary T cells from cord blood	blood
31	chr7:21540200-21543600	Strong transcription	Primary B cells from peripheral blood	blood
32	chr7:21540200-21544600	Strong transcription	Ovary	ovary
33	chr7:21540600-21543400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr7:21540600-21550800	Weak transcription	Fetal Lung	lung
35	chr7:21540600-21551600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr7:21540600-21554400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr7:21540800-21543800	Weak transcription	Brain Germinal Matrix	brain
38	chr7:21540800-21544200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr7:21540800-21545200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr7:21540800-21551400	Weak transcription	Brain Anterior Caudate	brain
41	chr7:21541000-21543400	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr7:21541000-21554800	Weak transcription	Lung	lung
43	chr7:21541200-21543000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr7:21541400-21543400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr7:21541400-21544000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr7:21541600-21544000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr7:21541600-21547000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr7:21541600-21547800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
49	chr7:21542000-21544000	Weak transcription	Fetal Thymus	thymus
50	chr7:21542000-21544400	Strong transcription	Primary T cells fromperipheralblood	blood

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