Variant report

Variant	rs17659220
Chromosome Location	chr15:39110325-39110326
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:38999832..39000780-chr15:39109707..39110440,2	MCF-7	breast:
2	chr15:39109788..39110560-chr15:39464020..39464923,3	K562	blood:
3	chr15:39109578..39110474-chr15:39145706..39146406,3	MCF-7	breast:
4	chr15:39060876..39061871-chr15:39109578..39110390,2	MCF-7	breast:
5	chr15:39109626..39110574-chr15:39283075..39284008,7	MCF-7	breast:
6	chr15:39108039..39110943-chr15:39463087..39465051,2	MCF-7	breast:
7	chr15:39109782..39110594-chr15:39145267..39146966,11	MCF-7	breast:
8	chr15:39109610..39110793-chr15:39283014..39284012,10	MCF-7	breast:
9	chr15:38999758..39000677-chr15:39109720..39110502,3	K562	blood:

No data

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs17601140	0.92[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17659166	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28702389	0.81[ASN][1000 genomes]
rs2912397	0.81[ASN][1000 genomes]
rs2929684	0.81[ASN][1000 genomes]
rs62007729	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62007730	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046994	chr15:38806163-39239014	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv832975	chr15:39011915-39227590	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1054810	chr15:39019900-39578526	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv542359	chr15:39019900-39578526	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv904087	chr15:39065424-39117186	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv510659	chr15:39072035-39148591	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv904088	chr15:39081717-39117186	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv904089	chr15:39104689-39117186	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39107400-39110600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr15:39109000-39110800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr15:39109200-39110400	Enhancers	Fetal Kidney	kidney
4	chr15:39109400-39110800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr15:39109400-39111000	Enhancers	GM12878-XiMat	blood
6	chr15:39109400-39111000	Enhancers	HSMM	muscle
7	chr15:39109600-39110400	Enhancers	HMEC	breast
8	chr15:39109600-39110600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr15:39109600-39110600	Enhancers	A549	lung
10	chr15:39109600-39110600	Enhancers	NH-A	brain
11	chr15:39109600-39110600	Enhancers	Osteobl	bone
12	chr15:39109600-39111200	Enhancers	Fetal Heart	heart
13	chr15:39109600-39111800	Enhancers	Fetal Stomach	stomach
14	chr15:39109800-39110400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr15:39109800-39110400	Enhancers	Fetal Intestine Large	intestine
16	chr15:39109800-39110400	Enhancers	NHLF	lung
17	chr15:39109800-39110600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:39109800-39110600	Enhancers	NHEK	skin
19	chr15:39109800-39110800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:39109800-39110800	Enhancers	HUVEC	blood vessel
21	chr15:39109800-39110800	Enhancers	NHDF-Ad	bronchial
22	chr15:39109800-39111200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr15:39109800-39112600	Enhancers	Fetal Lung	lung
24	chr15:39110000-39110400	Enhancers	Primary B cells from peripheral blood	blood
25	chr15:39110000-39110400	Enhancers	Primary T cells fromperipheralblood	blood
26	chr15:39110000-39110400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr15:39110000-39110400	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr15:39110000-39110400	Active TSS	Brain Substantia Nigra	brain
29	chr15:39110000-39110400	Enhancers	Colon Smooth Muscle	Colon
30	chr15:39110000-39110400	Enhancers	Placenta	Placenta
31	chr15:39110000-39110400	Enhancers	Ovary	ovary
32	chr15:39110000-39110400	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr15:39110000-39110400	Flanking Active TSS	Hela-S3	cervix
34	chr15:39110000-39110600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:39110000-39110600	Enhancers	Fetal Muscle Leg	muscle
36	chr15:39110000-39110800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr15:39110000-39110800	Enhancers	Fetal Muscle Trunk	muscle
38	chr15:39110200-39110400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
39	chr15:39110200-39110400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr15:39110200-39110400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr15:39110200-39110400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:39110200-39110400	Flanking Active TSS	Brain Angular Gyrus	brain
43	chr15:39110200-39110400	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr15:39110200-39110400	Active TSS	Brain Cingulate Gyrus	brain
45	chr15:39110200-39110400	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr15:39110200-39110600	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr15:39110200-39110600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:39110200-39110600	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr15:39110200-39110600	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr15:39110200-39110600	Enhancers	Rectal Smooth Muscle	rectum

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