Variant report

Variant	rs2303579
Chromosome Location	chr15:56152729-56152730
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56142489..56144203-chr15:56152079..56154618,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10459621	0.86[JPT][hapmap]
rs10518824	0.84[ASN][1000 genomes]
rs10518830	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs12441843	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs12593593	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs12913186	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553739	0.86[JPT][hapmap]
rs16976618	0.83[ASN][1000 genomes]
rs16976638	0.83[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs16976648	0.83[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs16976652	0.86[JPT][hapmap]
rs1863757	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1863758	1.00[ASN][1000 genomes]
rs1912405	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1912406	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1912407	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2175236	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2303580	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414448	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414449	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2438128	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57195161	0.85[ASN][1000 genomes]
rs60755985	0.86[ASN][1000 genomes]
rs62043794	0.82[ASN][1000 genomes]
rs6493824	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67387007	0.86[ASN][1000 genomes]
rs67497103	0.86[ASN][1000 genomes]
rs7162927	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170158	0.86[JPT][hapmap]
rs7170900	0.86[JPT][hapmap]
rs7177177	0.86[JPT][hapmap]
rs72732270	0.86[ASN][1000 genomes]
rs7497861	0.86[JPT][hapmap]
rs8033275	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8033577	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9806347	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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	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:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56116800-56162200	Weak transcription	Fetal Heart	heart
2	chr15:56122600-56153800	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr15:56122600-56154800	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr15:56122600-56156600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr15:56122800-56156000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr15:56127200-56155400	Strong transcription	Osteobl	bone
7	chr15:56127200-56155800	Strong transcription	HSMM	muscle
8	chr15:56129000-56157400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr15:56132000-56164800	Weak transcription	Small Intestine	intestine
10	chr15:56133600-56154400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr15:56134400-56156600	Weak transcription	Colon Smooth Muscle	Colon
12	chr15:56135000-56156600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr15:56138200-56161800	Weak transcription	K562	blood
14	chr15:56138600-56154400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:56138800-56152800	Weak transcription	GM12878-XiMat	blood
16	chr15:56139400-56155400	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr15:56139600-56153200	Strong transcription	NHEK	skin
18	chr15:56140200-56155600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:56142800-56153200	Strong transcription	Stomach Smooth Muscle	stomach
20	chr15:56142800-56155400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr15:56145800-56153000	Strong transcription	Fetal Intestine Small	intestine
22	chr15:56145800-56155400	Strong transcription	Fetal Intestine Large	intestine
23	chr15:56146000-56153000	Strong transcription	Fetal Stomach	stomach
24	chr15:56146200-56155000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:56146400-56155600	Strong transcription	Liver	Liver
26	chr15:56147200-56154800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:56148000-56160400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr15:56148200-56154400	Weak transcription	Thymus	Thymus
29	chr15:56148200-56155000	Weak transcription	Pancreas	Pancrea
30	chr15:56148200-56174400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:56148600-56153200	Strong transcription	Hela-S3	cervix
32	chr15:56148800-56161800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr15:56149000-56163600	Weak transcription	Gastric	stomach
34	chr15:56149000-56164800	Weak transcription	Aorta	Aorta
35	chr15:56149000-56177600	Weak transcription	Spleen	Spleen
36	chr15:56149400-56154400	Strong transcription	A549	lung
37	chr15:56149600-56153000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:56149600-56153600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr15:56150000-56153000	Strong transcription	Primary hematopoietic stem cells	blood
40	chr15:56150000-56153000	Strong transcription	Fetal Muscle Leg	muscle
41	chr15:56150000-56153000	Strong transcription	Psoas Muscle	Psoas
42	chr15:56150000-56153800	Strong transcription	HMEC	breast
43	chr15:56150000-56154400	Strong transcription	NH-A	brain
44	chr15:56150000-56155400	Strong transcription	Placenta	Placenta
45	chr15:56150200-56152800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:56150200-56153000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:56150200-56153000	Strong transcription	Primary T cells from cord blood	blood
48	chr15:56150200-56153000	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr15:56150200-56153000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr15:56150200-56153200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links