Variant report

Variant	rs2439923
Chromosome Location	chr15:57298255-57298256
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1652733	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs213154	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2243575	0.87[AFR][1000 genomes]
rs2430963	1.00[AMR][1000 genomes]
rs2435898	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2435899	0.81[AFR][1000 genomes]
rs2435900	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2435901	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2435902	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2435904	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2439924	0.81[AFR][1000 genomes]
rs2543676	1.00[AMR][1000 genomes]
rs2566839	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2566841	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2566847	0.94[AFR][1000 genomes]
rs2566852	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2585074	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2585079	0.81[AFR][1000 genomes]
rs2585085	0.87[AFR][1000 genomes]
rs2585092	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2585095	0.87[AFR][1000 genomes]
rs2585096	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2585098	1.00[YRI][hapmap]
rs2585100	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2585101	0.87[AFR][1000 genomes]
rs2585109	0.94[AFR][1000 genomes]
rs2585111	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2585119	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2585122	1.00[AMR][1000 genomes]
rs2593213	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2593224	1.00[AMR][1000 genomes]
rs2593227	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2593240	1.00[AMR][1000 genomes]
rs2615234	0.87[AFR][1000 genomes]
rs2615248	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2703591	1.00[AMR][1000 genomes]
rs2703603	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2703606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2703609	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2703615	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2703618	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2703622	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2733169	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2733173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2733175	0.94[AFR][1000 genomes]
rs2733186	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2733190	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2733193	1.00[AMR][1000 genomes]
rs2733196	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2733301	1.00[YRI][hapmap]
rs2733308	0.81[AFR][1000 genomes]
rs2733338	0.81[AFR][1000 genomes]
rs2733344	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2920271	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	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
5	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:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57269800-57304800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:57273000-57307200	Weak transcription	Fetal Intestine Small	intestine
3	chr15:57275400-57306200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr15:57276200-57313400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr15:57277000-57313400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:57279400-57300000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:57279600-57301800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr15:57279800-57300200	Weak transcription	Psoas Muscle	Psoas
9	chr15:57282000-57307400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:57282000-57315000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr15:57282200-57298600	Weak transcription	Ovary	ovary
12	chr15:57282200-57299400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr15:57282200-57308400	Weak transcription	Thymus	Thymus
14	chr15:57282200-57311000	Weak transcription	K562	blood
15	chr15:57282200-57315200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr15:57282600-57306200	Weak transcription	HepG2	liver
17	chr15:57284200-57310800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr15:57286000-57299400	Weak transcription	Primary T cells from cord blood	blood
19	chr15:57286000-57299800	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr15:57286000-57306200	Weak transcription	Fetal Intestine Large	intestine
21	chr15:57286000-57307400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:57286200-57307600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr15:57286200-57307600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:57286200-57312000	Weak transcription	HSMM	muscle
25	chr15:57286200-57314800	Weak transcription	Dnd41	blood
26	chr15:57286400-57309400	Weak transcription	Fetal Lung	lung
27	chr15:57288600-57300000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr15:57288800-57307400	Weak transcription	HMEC	breast
29	chr15:57289400-57304600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr15:57289400-57308000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr15:57289600-57315200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:57289600-57315600	Weak transcription	Fetal Muscle Leg	muscle
33	chr15:57289800-57315600	Weak transcription	Primary B cells from cord blood	blood
34	chr15:57292600-57298600	Weak transcription	Left Ventricle	heart
35	chr15:57292600-57300200	Weak transcription	Right Atrium	heart
36	chr15:57294200-57299000	Weak transcription	Fetal Heart	heart
37	chr15:57294200-57307400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:57294400-57311600	Weak transcription	GM12878-XiMat	blood
39	chr15:57295200-57313600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr15:57296000-57301400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr15:57296000-57307600	Weak transcription	Brain Substantia Nigra	brain
42	chr15:57296000-57308800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:57296000-57308800	Weak transcription	Brain Hippocampus Middle	brain
44	chr15:57296200-57299400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr15:57296200-57299800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr15:57296200-57301600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr15:57296200-57302800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr15:57296200-57303800	Weak transcription	HUVEC	blood vessel
49	chr15:57296200-57304600	Weak transcription	Brain Anterior Caudate	brain
50	chr15:57296200-57307400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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