Variant report

Variant	rs1925747
Chromosome Location	chr13:48762310-48762311
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1749976	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2182220	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406802	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2406804	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2765074	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2765075	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4942753	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4942754	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4942757	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs607954	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7329629	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7988534	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7989671	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7993868	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7994141	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7995410	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9534969	0.86[ASN][1000 genomes]
rs9534978	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9534979	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9534983	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534988	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv541766	chr13:48703229-48857639	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1047140	chr13:48703732-48765860	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv541767	chr13:48703732-48765860	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3327569	chr13:48743550-48798094	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1925747	SERP2	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48755200-48762800	Enhancers	Primary B cells from cord blood	blood
2	chr13:48755800-48763000	Enhancers	Primary B cells from peripheral blood	blood
3	chr13:48757400-48763200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr13:48758000-48763000	Enhancers	Fetal Thymus	thymus
5	chr13:48758000-48763200	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr13:48758000-48763400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr13:48758200-48762600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr13:48759200-48763200	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr13:48759400-48763200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr13:48760800-48762400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr13:48760800-48762600	Weak transcription	Small Intestine	intestine
12	chr13:48760800-48763200	Enhancers	Primary T cells fromperipheralblood	blood
13	chr13:48760800-48763200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr13:48760800-48763200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr13:48760800-48763800	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr13:48760800-48766200	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr13:48761000-48762600	Enhancers	Primary hematopoietic stem cells	blood
18	chr13:48761000-48762600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr13:48761000-48763400	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr13:48761200-48763800	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr13:48761400-48762600	Weak transcription	Thymus	Thymus
22	chr13:48761400-48762800	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr13:48761400-48762800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr13:48762000-48763200	Enhancers	Fetal Intestine Small	intestine
25	chr13:48762000-48763600	Enhancers	Primary T cells from cord blood	blood
26	chr13:48762000-48763600	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr13:48762200-48762600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr13:48762200-48763200	Enhancers	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links