Variant report

Variant	rs2388244
Chromosome Location	chr13:30373338-30373339
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11147398	0.83[YRI][hapmap]
rs17073936	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs182178	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1886170	0.93[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2234417	1.00[CHD][hapmap]
rs2388245	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278037	0.93[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs4083610	0.91[YRI][hapmap]
rs4769774	0.93[ASW][hapmap];0.88[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.90[LWK][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9314976	0.81[EUR][1000 genomes]
rs9506229	0.87[YRI][hapmap]
rs9506230	0.81[AFR][1000 genomes]
rs9508555	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs9508556	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9550494	0.87[YRI][hapmap]
rs9551744	0.87[YRI][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	nsv899961	chr13:30226924-30407273	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2388244	MTUS2	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30333600-30376200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr13:30360600-30374800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr13:30362400-30375600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr13:30363400-30375400	Weak transcription	Lung	lung
5	chr13:30363800-30385000	Weak transcription	Left Ventricle	heart
6	chr13:30365800-30383200	Weak transcription	Ovary	ovary
7	chr13:30366000-30375200	Weak transcription	Gastric	stomach
8	chr13:30366000-30375600	Weak transcription	Brain Angular Gyrus	brain
9	chr13:30366200-30381400	Weak transcription	Stomach Mucosa	stomach
10	chr13:30368000-30375200	Weak transcription	Brain Substantia Nigra	brain
11	chr13:30368200-30375400	Weak transcription	Brain Anterior Caudate	brain
12	chr13:30368200-30375400	Weak transcription	Brain Hippocampus Middle	brain
13	chr13:30369000-30375800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr13:30371000-30376000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr13:30371200-30375800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr13:30371800-30374200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr13:30371800-30375800	Weak transcription	Osteobl	bone
18	chr13:30372000-30374200	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr13:30372400-30374200	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr13:30372400-30374200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr13:30372400-30375000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr13:30372400-30375000	Weak transcription	Psoas Muscle	Psoas
23	chr13:30372600-30373400	Enhancers	Small Intestine	intestine
24	chr13:30372600-30374000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr13:30372800-30373400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr13:30372800-30373400	Weak transcription	Adipose Nuclei	Adipose
27	chr13:30372800-30378000	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr13:30372800-30378000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr13:30373000-30373800	Enhancers	Primary T cells from cord blood	blood
30	chr13:30373000-30374200	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr13:30373000-30374400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr13:30373000-30377800	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr13:30373200-30373400	Enhancers	H9 Cell Line	embryonic stem cell
34	chr13:30373200-30373400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr13:30373200-30373400	Enhancers	Primary T cells fromperipheralblood	blood
36	chr13:30373200-30373400	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr13:30373200-30373400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr13:30373200-30373600	Enhancers	Fetal Thymus	thymus
39	chr13:30373200-30373800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr13:30373200-30373800	Enhancers	Dnd41	blood
41	chr13:30373200-30374600	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr13:30373200-30376600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr13:30373200-30377600	Enhancers	HUES6 Cell Line	embryonic stem cell

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