Variant report

Variant	rs17238482
Chromosome Location	chr15:56154942-56154943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11550869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12898553	1.00[ASN][1000 genomes]
rs12902644	0.85[JPT][hapmap]
rs17238461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17238489	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17819282	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17819300	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4774833	0.85[JPT][hapmap]
rs55782406	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62043760	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62043761	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62043763	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62043764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62043792	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62043793	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62043796	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62043801	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62043802	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62043810	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62043815	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62043816	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62043847	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62043854	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62046605	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs62046606	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62046641	0.96[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs62046642	0.96[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs62046643	0.96[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs62046644	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62046645	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62046648	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62046649	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62046650	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7174459	0.85[JPT][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	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv833017	chr15:55965957-56157912	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56116800-56162200	Weak transcription	Fetal Heart	heart
2	chr15:56122600-56156600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr15:56122800-56156000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr15:56127200-56155400	Strong transcription	Osteobl	bone
5	chr15:56127200-56155800	Strong transcription	HSMM	muscle
6	chr15:56129000-56157400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:56132000-56164800	Weak transcription	Small Intestine	intestine
8	chr15:56134400-56156600	Weak transcription	Colon Smooth Muscle	Colon
9	chr15:56135000-56156600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:56138200-56161800	Weak transcription	K562	blood
11	chr15:56139400-56155400	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr15:56140200-56155600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:56142800-56155400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr15:56145800-56155400	Strong transcription	Fetal Intestine Large	intestine
15	chr15:56146200-56155000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr15:56146400-56155600	Strong transcription	Liver	Liver
17	chr15:56148000-56160400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:56148200-56155000	Weak transcription	Pancreas	Pancrea
19	chr15:56148200-56174400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:56148800-56161800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:56149000-56163600	Weak transcription	Gastric	stomach
22	chr15:56149000-56164800	Weak transcription	Aorta	Aorta
23	chr15:56149000-56177600	Weak transcription	Spleen	Spleen
24	chr15:56150000-56155400	Strong transcription	Placenta	Placenta
25	chr15:56150400-56155400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:56150400-56155600	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr15:56152000-56155200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:56152400-56156600	Weak transcription	Fetal Kidney	kidney
29	chr15:56152400-56164800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr15:56152600-56155400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr15:56152800-56155800	Weak transcription	Fetal Thymus	thymus
32	chr15:56152800-56165000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr15:56152800-56174600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:56153000-56155000	Weak transcription	Right Ventricle	heart
35	chr15:56153000-56155600	Weak transcription	Fetal Stomach	stomach
36	chr15:56153000-56157800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr15:56153000-56157800	Weak transcription	Left Ventricle	heart
38	chr15:56153000-56157800	Weak transcription	NHLF	lung
39	chr15:56153000-56160400	Weak transcription	Primary T cells from cord blood	blood
40	chr15:56153000-56161000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:56153000-56161000	Weak transcription	HepG2	liver
42	chr15:56153000-56163200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr15:56153000-56163800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr15:56153000-56164800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr15:56153000-56164800	Weak transcription	Ovary	ovary
46	chr15:56153000-56167400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:56153000-56174000	Weak transcription	Primary hematopoietic stem cells	blood
48	chr15:56153000-56174400	Weak transcription	HSMMtube	muscle
49	chr15:56153000-56174800	Weak transcription	Fetal Intestine Small	intestine
50	chr15:56153000-56176400	Weak transcription	Esophagus	oesophagus

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