Variant report

Variant	rs9506229
Chromosome Location	chr13:30367959-30367960
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1058650	0.91[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs11147398	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12872400	0.82[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs1323931	0.87[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs1410110	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1772727	0.82[AFR][1000 genomes]
rs1854176	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1886170	0.91[YRI][hapmap]
rs1927193	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2025604	0.84[ASN][1000 genomes]
rs2182129	0.87[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs2234416	0.91[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs2388244	0.87[YRI][hapmap]
rs2388246	0.87[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2388247	0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2761938	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2761939	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2761940	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs278034	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs278037	0.91[YRI][hapmap]
rs35541102	0.89[ASN][1000 genomes]
rs4083610	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4238128	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4265673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4297554	0.91[ASN][1000 genomes]
rs4769772	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4769774	0.91[YRI][hapmap]
rs4769775	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6490429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490430	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72623487	0.80[ASN][1000 genomes]
rs7320474	0.91[ASN][1000 genomes]
rs7326253	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7330356	0.95[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7335148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7342470	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs765404	0.84[ASN][1000 genomes]
rs7981622	0.87[ASN][1000 genomes]
rs7995666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9314972	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9314973	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9314974	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9314978	0.91[ASN][1000 genomes]
rs9506226	0.89[ASN][1000 genomes]
rs9506230	0.85[AFR][1000 genomes]
rs9506231	0.87[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs9506233	0.87[ASN][1000 genomes]
rs9508550	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9508553	0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs9508554	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9508555	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs9508557	0.91[ASN][1000 genomes]
rs9508558	0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs9508559	0.89[ASN][1000 genomes]
rs9508560	0.85[ASN][1000 genomes]
rs9508564	0.87[ASN][1000 genomes]
rs9508568	0.93[ASN][1000 genomes]
rs9550494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9551739	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9551741	0.81[ASN][1000 genomes]
rs9551744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9551751	0.91[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs9578136	0.87[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs9578139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30333200-30368200	Weak transcription	Aorta	Aorta
2	chr13:30333600-30376200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr13:30341200-30373200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr13:30360400-30368000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr13:30360600-30368000	Weak transcription	Fetal Intestine Large	intestine
6	chr13:30360600-30374800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr13:30361800-30373000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr13:30362400-30370800	Weak transcription	NHDF-Ad	bronchial
9	chr13:30362400-30375600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr13:30362600-30372600	Weak transcription	Small Intestine	intestine
11	chr13:30362800-30368400	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr13:30363200-30373200	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr13:30363400-30368000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr13:30363400-30372200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr13:30363400-30375400	Weak transcription	Lung	lung
16	chr13:30363800-30385000	Weak transcription	Left Ventricle	heart
17	chr13:30364200-30372200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr13:30365000-30368200	Enhancers	Brain Anterior Caudate	brain
19	chr13:30365000-30373000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr13:30365200-30370600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr13:30365400-30368000	Enhancers	Brain Substantia Nigra	brain
22	chr13:30365600-30368400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr13:30365800-30383200	Weak transcription	Ovary	ovary
24	chr13:30366000-30368000	Weak transcription	Pancreas	Pancrea
25	chr13:30366000-30368800	Weak transcription	Liver	Liver
26	chr13:30366000-30375200	Weak transcription	Gastric	stomach
27	chr13:30366000-30375600	Weak transcription	Brain Angular Gyrus	brain
28	chr13:30366200-30381400	Weak transcription	Stomach Mucosa	stomach
29	chr13:30366600-30369400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr13:30366800-30370400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr13:30366800-30370600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr13:30367000-30370800	Weak transcription	Osteobl	bone
33	chr13:30367200-30368200	Enhancers	Brain Hippocampus Middle	brain
34	chr13:30367200-30368800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr13:30367200-30368800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr13:30367600-30369000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr13:30367600-30371600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr13:30367800-30368000	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr13:30367800-30368200	Active TSS	Duodenum Mucosa	Duodenum
40	chr13:30367800-30369200	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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