Variant report

Variant	rs11858599
Chromosome Location	chr15:55838506-55838507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:55832795..55834702-chr15:55836212..55838623,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1051506	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11630020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11634048	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11634055	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11634657	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11634919	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11635072	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11635978	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11637574	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11637694	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11638846	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11639329	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11639446	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11854594	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11858624	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17238269	1.00[YRI][hapmap]
rs1926	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2414420	0.86[AFR][1000 genomes]
rs34694682	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4774791	0.88[CEU][hapmap];0.86[MEX][hapmap]
rs62020018	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62020019	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62020020	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62020021	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62020022	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62020023	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62020033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62020034	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62020035	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62020037	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62020038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62020039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62020041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62020043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62020044	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62020045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62020047	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62020057	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62020058	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62021860	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62021861	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62021862	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs62021863	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62021865	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs62021866	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62021867	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62021868	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62021869	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62021870	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62021872	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs62021873	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62021874	0.94[EUR][1000 genomes]
rs62021876	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62021877	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62021878	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62021879	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62021880	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7181070	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7182121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1040917	chr15:55562940-55943942	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv531054	chr15:55571230-55914205	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers 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 miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv1041635	chr15:55658171-55943942	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv833016	chr15:55749169-55897906	Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1049774	chr15:55759573-56044600	Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55819200-55844200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:55831200-55839000	Weak transcription	NH-A	brain
3	chr15:55831200-55844800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr15:55831200-55846800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:55834000-55845000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:55835200-55844800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:55836000-55846400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr15:55836200-55845200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr15:55836400-55840800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:55836400-55844800	Weak transcription	Fetal Brain Male	brain
11	chr15:55836600-55840000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:55836600-55840200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:55837000-55839800	Weak transcription	Adipose Nuclei	Adipose
14	chr15:55837200-55844800	Weak transcription	NHLF	lung
15	chr15:55837400-55838600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:55837400-55838800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:55837400-55839000	Weak transcription	HUVEC	blood vessel
18	chr15:55837400-55840000	Weak transcription	Fetal Intestine Large	intestine
19	chr15:55837400-55842400	Weak transcription	Brain Germinal Matrix	brain
20	chr15:55837600-55839200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:55837600-55840000	Weak transcription	Right Ventricle	heart
22	chr15:55837600-55843200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:55837800-55839000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:55837800-55840200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr15:55838000-55839200	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:55838000-55839400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:55838200-55838600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:55838200-55838600	Strong transcription	Aorta	Aorta
29	chr15:55838200-55838600	Strong transcription	Fetal Brain Female	brain
30	chr15:55838200-55838600	Strong transcription	Fetal Muscle Leg	muscle
31	chr15:55838200-55838600	Strong transcription	Fetal Stomach	stomach
32	chr15:55838200-55838600	ZNF genes & repeats	Pancreas	Pancrea
33	chr15:55838200-55838600	Strong transcription	Placenta Amnion	Placenta Amnion
34	chr15:55838200-55838600	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr15:55838200-55838800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:55838200-55838800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr15:55838200-55838800	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr15:55838200-55838800	Strong transcription	HSMMtube	muscle
39	chr15:55838200-55839000	Strong transcription	Ovary	ovary
40	chr15:55838200-55839000	Strong transcription	Osteobl	bone
41	chr15:55838200-55839200	Strong transcription	Fetal Muscle Trunk	muscle
42	chr15:55838200-55839200	Strong transcription	Left Ventricle	heart
43	chr15:55838200-55839200	Strong transcription	A549	lung
44	chr15:55838200-55839200	Genic enhancers	HSMM	muscle
45	chr15:55838200-55839400	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr15:55838200-55839400	Strong transcription	NHDF-Ad	bronchial
47	chr15:55838200-55839800	Strong transcription	Stomach Smooth Muscle	stomach
48	chr15:55838400-55839400	Strong transcription	Fetal Lung	lung

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