Variant report

Variant	rs230946
Chromosome Location	chr17:15137479-15137480
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	chr17:15136279..15139098-chr17:15139900..15142185,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238806	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs13422	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs179520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1860295	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs192046	0.96[EUR][1000 genomes]
rs230913	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs230914	0.83[EUR][1000 genomes]
rs230931	0.94[EUR][1000 genomes]
rs230934	0.96[EUR][1000 genomes]
rs230935	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs230936	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs230937	0.96[EUR][1000 genomes]
rs230939	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs230941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs230942	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs230943	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs230944	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230949	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs230950	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs231025	0.81[CHB][hapmap]
rs231028	0.86[CHB][hapmap]
rs231030	0.85[CHB][hapmap]
rs2531951	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066329	chr17:14983674-15294071	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv543212	chr17:14983674-15294071	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15131200-15141600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr17:15131600-15138000	Genic enhancers	Right Ventricle	heart
3	chr17:15131600-15139600	Weak transcription	Liver	Liver
4	chr17:15131600-15145600	Strong transcription	Fetal Muscle Trunk	muscle
5	chr17:15131800-15139800	Strong transcription	Fetal Stomach	stomach
6	chr17:15132200-15139400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr17:15132200-15144400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr17:15132200-15158800	Weak transcription	Hela-S3	cervix
9	chr17:15132400-15143200	Strong transcription	HSMMtube	muscle
10	chr17:15132600-15138400	Strong transcription	Aorta	Aorta
11	chr17:15132600-15140000	Genic enhancers	Left Ventricle	heart
12	chr17:15132600-15142800	Weak transcription	Esophagus	oesophagus
13	chr17:15132800-15139600	Strong transcription	Fetal Lung	lung
14	chr17:15134000-15140400	Weak transcription	NH-A	brain
15	chr17:15134400-15140600	Genic enhancers	Brain Cingulate Gyrus	brain
16	chr17:15134400-15151000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr17:15134600-15139000	Genic enhancers	Brain Anterior Caudate	brain
18	chr17:15134600-15140200	Genic enhancers	Brain Substantia Nigra	brain
19	chr17:15134600-15143200	Strong transcription	HSMM	muscle
20	chr17:15134800-15139000	Enhancers	K562	blood
21	chr17:15134800-15140200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr17:15134800-15140400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr17:15135000-15137600	Enhancers	Spleen	Spleen
24	chr17:15135200-15137800	Enhancers	Right Atrium	heart
25	chr17:15135200-15144800	Genic enhancers	Colon Smooth Muscle	Colon
26	chr17:15135400-15137800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr17:15135400-15140600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr17:15135600-15137600	Strong transcription	Colonic Mucosa	Colon
29	chr17:15135600-15137800	Genic enhancers	Osteobl	bone
30	chr17:15135600-15138800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
31	chr17:15135600-15139000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
32	chr17:15135600-15140800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr17:15135600-15142400	Genic enhancers	NHDF-Ad	bronchial
34	chr17:15135600-15143400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr17:15135800-15137600	Genic enhancers	Ovary	ovary
36	chr17:15135800-15137800	Genic enhancers	Stomach Smooth Muscle	stomach
37	chr17:15135800-15138000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr17:15135800-15138000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr17:15135800-15139000	Genic enhancers	Duodenum Smooth Muscle	Duodenum
40	chr17:15135800-15140000	Genic enhancers	Brain Hippocampus Middle	brain
41	chr17:15135800-15141800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr17:15135800-15151200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr17:15135800-15160200	Weak transcription	Pancreas	Pancrea
44	chr17:15136000-15137600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr17:15136000-15137600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr17:15136000-15137600	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr17:15136000-15137800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr17:15136000-15137800	Enhancers	HMEC	breast
49	chr17:15136000-15138000	Genic enhancers	Adipose Nuclei	Adipose
50	chr17:15136000-15138400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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