Variant report

Variant	rs56009713
Chromosome Location	chr15:99662254-99662255
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	chr15:99660192..99663154-chr15:99718347..99720346,2	MCF-7	breast:
2	chr15:99652267..99657709-chr15:99661798..99664247,5	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12324825	0.81[ASN][1000 genomes]
rs12911794	0.90[ASN][1000 genomes]
rs12915572	0.82[ASN][1000 genomes]
rs1670237	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1810091	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1965866	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1965867	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242076	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34567778	0.88[EUR][1000 genomes]
rs34878632	0.84[EUR][1000 genomes]
rs55905808	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7162579	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7164548	0.80[ASN][1000 genomes]
rs8029732	0.81[ASN][1000 genomes]
rs8032817	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8037159	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8038845	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8041213	0.92[ASN][1000 genomes]
rs906760	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS 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	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS 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	60 gene(s)	inside rSNPs	diseases
4	nsv533375	chr15:99443534-99696221	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1050982	chr15:99450004-99725825	Enhancers Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv530685	chr15:99452377-99713365	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1038870	chr15:99510479-99768374	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
12	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
13	nsv1051782	chr15:99621061-99792967	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers 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	26 gene(s)	inside rSNPs	diseases
14	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
16	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
17	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99646400-99663200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:99646800-99663600	Weak transcription	Ovary	ovary
3	chr15:99646800-99663600	Weak transcription	Spleen	Spleen
4	chr15:99647000-99663200	Weak transcription	HSMM	muscle
5	chr15:99647600-99672400	Weak transcription	Esophagus	oesophagus
6	chr15:99648000-99663200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr15:99648200-99663000	Weak transcription	NHDF-Ad	bronchial
8	chr15:99648200-99663200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr15:99649000-99663800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:99650400-99663400	Weak transcription	HSMMtube	muscle
11	chr15:99650600-99663400	Weak transcription	Colonic Mucosa	Colon
12	chr15:99651200-99663200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:99651200-99663800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:99651400-99663200	Weak transcription	NH-A	brain
15	chr15:99651800-99662800	Weak transcription	Primary T cells from cord blood	blood
16	chr15:99651800-99663200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:99651800-99663200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:99652000-99669800	Weak transcription	Thymus	Thymus
19	chr15:99652200-99663600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:99652400-99663200	Weak transcription	Fetal Intestine Large	intestine
21	chr15:99654200-99663600	Weak transcription	Pancreas	Pancrea
22	chr15:99655000-99663200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:99655400-99663000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr15:99655400-99663200	Weak transcription	HepG2	liver
25	chr15:99655400-99663200	Weak transcription	NHLF	lung
26	chr15:99655400-99664400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr15:99655600-99663200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr15:99655600-99663200	Weak transcription	Fetal Intestine Small	intestine
29	chr15:99656200-99663400	Enhancers	Rectal Smooth Muscle	rectum
30	chr15:99657800-99663600	Weak transcription	Gastric	stomach
31	chr15:99658600-99663400	Enhancers	Fetal Heart	heart
32	chr15:99658800-99663200	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr15:99659600-99662800	Weak transcription	Lung	lung
34	chr15:99659800-99663200	Weak transcription	Aorta	Aorta
35	chr15:99660000-99663200	Weak transcription	Adipose Nuclei	Adipose
36	chr15:99660400-99662800	Enhancers	Brain Angular Gyrus	brain
37	chr15:99660400-99663600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:99660600-99662600	Enhancers	Brain Substantia Nigra	brain
39	chr15:99660600-99663600	Enhancers	Brain Hippocampus Middle	brain
40	chr15:99660600-99671600	Weak transcription	Liver	Liver
41	chr15:99661000-99663200	Weak transcription	Fetal Muscle Leg	muscle
42	chr15:99661000-99663200	Enhancers	Hela-S3	cervix
43	chr15:99661000-99663600	Weak transcription	Placenta	Placenta
44	chr15:99661000-99666400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:99661200-99663200	Enhancers	Colon Smooth Muscle	Colon
46	chr15:99661200-99663600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr15:99661200-99663600	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr15:99661400-99663200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:99661600-99662400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
50	chr15:99661600-99663200	Weak transcription	Psoas Muscle	Psoas

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