Variant report

Variant	rs2566841
Chromosome Location	chr15:57239491-57239492
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57210198..57214861-chr15:57238728..57241582,5	K562	blood:
2	chr15:57222920..57225645-chr15:57236445..57240161,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140262	Chromatin interaction
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

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	0.82[AFR][1000 genomes]
rs2430963	1.00[AMR][1000 genomes]
rs2435898	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2435899	0.88[AFR][1000 genomes]
rs2435900	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2435901	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2435902	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2435904	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2439923	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2439924	0.88[AFR][1000 genomes]
rs2543676	1.00[AMR][1000 genomes]
rs2566839	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2566847	0.88[AFR][1000 genomes]
rs2566852	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2585074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2585079	0.88[AFR][1000 genomes]
rs2585085	0.82[AFR][1000 genomes]
rs2585092	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2585095	0.82[AFR][1000 genomes]
rs2585096	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2585098	1.00[YRI][hapmap]
rs2585100	1.00[AMR][1000 genomes]
rs2585101	0.82[AFR][1000 genomes]
rs2585109	0.88[AFR][1000 genomes]
rs2585111	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2585119	1.00[AMR][1000 genomes]
rs2585122	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2593213	1.00[YRI][hapmap]
rs2593227	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2615234	0.82[AFR][1000 genomes]
rs2703603	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2703606	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2703609	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2703618	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2703622	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2733169	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2733173	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2733175	0.88[AFR][1000 genomes]
rs2733186	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2733190	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2733193	1.00[AMR][1000 genomes]
rs2733196	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2920271	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][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	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57212400-57256000	Weak transcription	Pancreas	Pancrea
2	chr15:57212600-57241000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:57213200-57256000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:57216400-57241800	Weak transcription	Fetal Brain Male	brain
5	chr15:57222600-57250200	Weak transcription	NH-A	brain
6	chr15:57222800-57240800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr15:57222800-57255000	Weak transcription	HMEC	breast
8	chr15:57223200-57240400	Weak transcription	Aorta	Aorta
9	chr15:57224600-57248600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr15:57225000-57244200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr15:57225000-57249000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:57226400-57242000	Weak transcription	HUVEC	blood vessel
13	chr15:57227000-57249800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr15:57227600-57260600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:57228000-57242400	Weak transcription	Fetal Intestine Small	intestine
16	chr15:57228200-57260600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr15:57229400-57255800	Weak transcription	Fetal Stomach	stomach
18	chr15:57231200-57240800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr15:57232000-57256000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr15:57232200-57240000	Weak transcription	NHLF	lung
21	chr15:57233000-57250200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:57233800-57242000	Weak transcription	Ovary	ovary
23	chr15:57234200-57240800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr15:57234400-57249000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr15:57236000-57239800	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr15:57236200-57239800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:57236200-57240400	Weak transcription	Osteobl	bone
28	chr15:57236800-57249800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr15:57237000-57242000	Weak transcription	Brain Anterior Caudate	brain
30	chr15:57237200-57240400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr15:57237200-57241800	Weak transcription	Fetal Heart	heart
32	chr15:57237600-57239600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
33	chr15:57238200-57239600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:57238200-57240400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr15:57238200-57240600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr15:57238200-57240600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr15:57238200-57240800	Weak transcription	Fetal Lung	lung
38	chr15:57238200-57240800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr15:57238200-57249000	Weak transcription	HSMM	muscle
40	chr15:57238400-57239600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:57238400-57239800	Weak transcription	Dnd41	blood
42	chr15:57238400-57240600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr15:57238400-57240800	Weak transcription	Adipose Nuclei	Adipose
44	chr15:57238400-57241200	Weak transcription	Fetal Kidney	kidney
45	chr15:57238400-57241600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr15:57238400-57242800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:57238400-57243400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr15:57238400-57247800	Weak transcription	NHDF-Ad	bronchial
49	chr15:57238400-57249000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr15:57238400-57256200	Weak transcription	K562	blood

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