Variant report

Variant	rs17073454
Chromosome Location	chr13:30039629-30039630
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:30031933..30034245-chr13:30038590..30040708,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs17073440	1.00[AMR][1000 genomes]
rs17073446	0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs17073450	0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17073453	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17073456	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17073458	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17073460	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17073464	0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs17073469	0.92[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17073508	1.00[AMR][1000 genomes]
rs17073523	1.00[MEX][hapmap]
rs17658712	0.92[YRI][hapmap]
rs17658743	0.90[YRI][hapmap]
rs2036974	1.00[MEX][hapmap]
rs2992385	1.00[MEX][hapmap]
rs4503648	0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57888514	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59895574	1.00[AMR][1000 genomes]
rs59903271	1.00[AMR][1000 genomes]
rs61119342	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7335252	0.92[YRI][hapmap]
rs7336242	0.84[YRI][hapmap]
rs73444083	1.00[AMR][1000 genomes]
rs73444089	1.00[AMR][1000 genomes]
rs73446117	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446120	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446124	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446125	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446128	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446130	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446133	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446135	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446137	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446140	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446144	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446147	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446154	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446158	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446160	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446162	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446165	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74044806	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74044808	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7984642	1.00[AMR][1000 genomes]
rs7985018	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7985850	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7986480	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7986808	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7987266	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8002833	0.83[YRI][hapmap]
rs8003005	0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427927	chr13:29729315-30062054	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv983696	chr13:30034016-30090454	Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30015200-30054800	Weak transcription	Dnd41	blood
2	chr13:30034600-30039800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr13:30036000-30040400	Enhancers	Left Ventricle	heart
4	chr13:30036600-30040200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr13:30036800-30043200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr13:30038200-30041400	Enhancers	Fetal Muscle Leg	muscle
7	chr13:30038600-30040800	Enhancers	HMEC	breast
8	chr13:30038800-30041000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr13:30039000-30039800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr13:30039000-30040600	Enhancers	Spleen	Spleen
11	chr13:30039000-30041000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr13:30039200-30040400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr13:30039200-30040600	Enhancers	K562	blood
14	chr13:30039200-30041600	Enhancers	Fetal Muscle Trunk	muscle
15	chr13:30039400-30040000	Enhancers	Aorta	Aorta
16	chr13:30039400-30040400	Enhancers	Right Atrium	heart
17	chr13:30039400-30040400	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr13:30039400-30040600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr13:30039400-30040600	Flanking Active TSS	Fetal Heart	heart
20	chr13:30039400-30040600	Enhancers	Placenta Amnion	Placenta Amnion
21	chr13:30039400-30040600	Enhancers	Rectal Smooth Muscle	rectum
22	chr13:30039400-30040600	Enhancers	Right Ventricle	heart
23	chr13:30039600-30040000	Enhancers	Colon Smooth Muscle	Colon
24	chr13:30039600-30040200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr13:30039600-30040200	Enhancers	Ovary	ovary
26	chr13:30039600-30040400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr13:30039600-30040400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr13:30039600-30040400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr13:30039600-30040400	Enhancers	Fetal Intestine Large	intestine
30	chr13:30039600-30040400	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr13:30039600-30040400	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr13:30039600-30040600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr13:30039600-30040600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr13:30039600-30040600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr13:30039600-30040600	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr13:30039600-30040600	Enhancers	Fetal Stomach	stomach
37	chr13:30039600-30040600	Enhancers	HSMM	muscle
38	chr13:30039600-30040600	Enhancers	NH-A	brain
39	chr13:30039600-30040800	Enhancers	HSMMtube	muscle

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