Variant report

Variant	rs2435899
Chromosome Location	chr15:57272689-57272690
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	chr15:57265601..57267263-chr15:57271593..57273612,2	K562	blood:
2	chr15:57261844..57263544-chr15:57271380..57273128,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1652733	1.00[YRI][hapmap]
rs2243575	1.00[AMR][1000 genomes]
rs2435894	1.00[AMR][1000 genomes]
rs2435898	0.94[AFR][1000 genomes]
rs2435901	0.81[AFR][1000 genomes]
rs2435904	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2439923	0.81[AFR][1000 genomes]
rs2439924	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2566841	0.88[AFR][1000 genomes]
rs2566847	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2566852	0.81[AFR][1000 genomes]
rs2585074	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2585079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2585085	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2585095	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2585101	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2585109	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2585113	1.00[AMR][1000 genomes]
rs2585122	1.00[YRI][hapmap]
rs2593245	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2593247	0.93[AFR][1000 genomes]
rs2593253	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs2615234	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2615239	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2615245	0.93[AFR][1000 genomes]
rs2615247	1.00[AMR][1000 genomes]
rs2615248	0.87[AFR][1000 genomes]
rs2703581	1.00[AMR][1000 genomes]
rs2703585	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2703603	0.81[AFR][1000 genomes]
rs2703606	0.81[AFR][1000 genomes]
rs2703611	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2703615	0.87[AFR][1000 genomes]
rs2703617	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2703621	1.00[AMR][1000 genomes]
rs2703622	0.81[AFR][1000 genomes]
rs2733173	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2733175	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2733184	1.00[AMR][1000 genomes]
rs2733308	1.00[AMR][1000 genomes]
rs2733338	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2920271	0.81[AFR][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	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv904250	chr15:57225766-57294085	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1052052	chr15:57232111-57344561	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv542394	chr15:57232111-57344561	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	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

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57256800-57277200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr15:57257200-57274600	Weak transcription	Adipose Nuclei	Adipose
3	chr15:57261200-57272800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr15:57261200-57279000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:57261400-57275000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr15:57262200-57280000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:57263800-57276000	Weak transcription	Lung	lung
8	chr15:57264200-57272800	Weak transcription	Right Atrium	heart
9	chr15:57264200-57272800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr15:57264800-57275000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr15:57264800-57275200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr15:57265000-57272800	Weak transcription	Brain Angular Gyrus	brain
13	chr15:57265400-57277000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:57266200-57274200	Weak transcription	Liver	Liver
15	chr15:57266400-57272800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr15:57266600-57272800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr15:57267000-57273200	Weak transcription	Dnd41	blood
18	chr15:57267000-57273400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr15:57267000-57274600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr15:57267400-57274000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr15:57269800-57273800	Enhancers	Brain Hippocampus Middle	brain
22	chr15:57269800-57275200	Weak transcription	Right Ventricle	heart
23	chr15:57269800-57276400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:57269800-57304800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:57270000-57272800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:57270000-57276800	Weak transcription	HSMMtube	muscle
27	chr15:57270000-57280200	Weak transcription	Fetal Brain Male	brain
28	chr15:57270600-57272800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:57270600-57272800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:57270800-57273000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:57270800-57273600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr15:57271000-57273000	Enhancers	NHDF-Ad	bronchial
33	chr15:57271000-57273000	Enhancers	NHEK	skin
34	chr15:57271000-57273600	Enhancers	K562	blood
35	chr15:57271000-57273800	Enhancers	Brain Cingulate Gyrus	brain
36	chr15:57271200-57273000	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr15:57271200-57273000	Enhancers	Osteobl	bone
38	chr15:57271200-57276200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr15:57271400-57275000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr15:57271400-57276400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr15:57271600-57273000	Enhancers	HSMM	muscle
42	chr15:57271600-57274400	Enhancers	Brain Anterior Caudate	brain
43	chr15:57271600-57275200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr15:57271600-57275800	Enhancers	Brain Substantia Nigra	brain
45	chr15:57271600-57276600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:57271800-57273800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:57271800-57275000	Weak transcription	HepG2	liver
48	chr15:57271800-57276600	Weak transcription	NHLF	lung
49	chr15:57272000-57273000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr15:57272000-57273000	Enhancers	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links