Variant report

Variant	rs12440729
Chromosome Location	chr15:57497961-57497962
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57491334..57495003-chr15:57497716..57500211,4	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs12437777	1.00[AFR][1000 genomes]
rs12438151	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12438244	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12438324	0.85[AMR][1000 genomes]
rs12438331	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12438428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12438464	1.00[AFR][1000 genomes]
rs12438782	0.88[AMR][1000 genomes]
rs12438893	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12439010	1.00[AFR][1000 genomes]
rs12439017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12439374	0.85[AMR][1000 genomes]
rs12440036	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12440116	0.84[EUR][1000 genomes]
rs12440699	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12440878	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12441239	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12441888	1.00[AFR][1000 genomes]
rs12441892	1.00[AFR][1000 genomes]
rs12442042	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12442326	1.00[AFR][1000 genomes]
rs12442521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12442879	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12443085	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1462157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17239047	1.00[AFR][1000 genomes]
rs17239068	1.00[AFR][1000 genomes]
rs17239089	1.00[AFR][1000 genomes]
rs17239187	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17239208	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs17239215	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs17239313	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17239522	0.85[AMR][1000 genomes]
rs17819755	1.00[AFR][1000 genomes]
rs17819779	1.00[AFR][1000 genomes]
rs17819809	1.00[AFR][1000 genomes]
rs17819839	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs17819886	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs17819946	1.00[AFR][1000 genomes]
rs17819994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17820006	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17820077	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17820119	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17820131	0.87[AMR][1000 genomes]
rs1816322	1.00[AFR][1000 genomes]
rs2126398	1.00[AFR][1000 genomes]
rs2414496	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4320591	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4514619	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs8031866	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv457164	chr15:57495060-57559387	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv569578	chr15:57495060-57559387	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57444400-57507400	Weak transcription	K562	blood
2	chr15:57453800-57524600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:57457200-57499400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr15:57458200-57505200	Strong transcription	Fetal Thymus	thymus
5	chr15:57478800-57526200	Weak transcription	Hela-S3	cervix
6	chr15:57479400-57524800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:57481800-57524600	Weak transcription	Right Ventricle	heart
8	chr15:57484800-57502000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr15:57485000-57501000	Weak transcription	Spleen	Spleen
10	chr15:57485000-57501800	Weak transcription	Lung	lung
11	chr15:57485000-57506200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:57485600-57505000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:57486800-57505800	Weak transcription	NHDF-Ad	bronchial
14	chr15:57487000-57524400	Weak transcription	Placenta	Placenta
15	chr15:57487200-57503000	Weak transcription	Liver	Liver
16	chr15:57487200-57511200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr15:57488200-57511600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr15:57489200-57506000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:57489400-57506200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:57490600-57505800	Weak transcription	NH-A	brain
21	chr15:57491000-57501400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr15:57491000-57505600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:57491000-57506000	Weak transcription	HMEC	breast
24	chr15:57491200-57508000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:57491400-57500800	Weak transcription	Thymus	Thymus
26	chr15:57491400-57501200	Weak transcription	Primary B cells from cord blood	blood
27	chr15:57491400-57503000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr15:57491400-57503000	Weak transcription	Primary T cells from cord blood	blood
29	chr15:57491400-57503200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:57491400-57505800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr15:57491400-57505800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr15:57491400-57506000	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr15:57491400-57506200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr15:57491400-57510000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr15:57491400-57510000	Weak transcription	Psoas Muscle	Psoas
36	chr15:57491400-57510200	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr15:57491400-57511200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr15:57491600-57498400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr15:57491600-57505200	Weak transcription	NHLF	lung
40	chr15:57491600-57506000	Weak transcription	Fetal Stomach	stomach
41	chr15:57491600-57508000	Weak transcription	HUVEC	blood vessel
42	chr15:57491600-57515200	Weak transcription	GM12878-XiMat	blood
43	chr15:57492000-57504200	Weak transcription	Brain Substantia Nigra	brain
44	chr15:57492000-57505200	Weak transcription	Fetal Kidney	kidney
45	chr15:57492400-57504200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr15:57492400-57504800	Weak transcription	Fetal Muscle Leg	muscle
47	chr15:57492400-57511600	Weak transcription	Left Ventricle	heart
48	chr15:57493600-57504800	Weak transcription	Brain Germinal Matrix	brain
49	chr15:57493600-57506000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr15:57494000-57504400	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links