Variant report

Variant	rs17073456
Chromosome Location	chr13:30040001-30040002
allele	G/T
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:
2	chr13:30004238..30007037-chr13:30039957..30042657,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs17073440	1.00[AMR][1000 genomes]
rs17073446	0.83[YRI][hapmap];0.86[AFR][1000 genomes]
rs17073450	0.82[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17073453	0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17073454	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	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs17073469	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17073508	1.00[AMR][1000 genomes]
rs17073523	1.00[MEX][hapmap]
rs17658712	0.84[YRI][hapmap]
rs17658743	0.80[YRI][hapmap]
rs2036974	1.00[MEX][hapmap]
rs2992385	1.00[MEX][hapmap]
rs4503648	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57888514	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59895574	1.00[AMR][1000 genomes]
rs59903271	1.00[AMR][1000 genomes]
rs61119342	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7335252	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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446154	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446158	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446160	0.94[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	0.91[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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

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:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30015200-30054800	Weak transcription	Dnd41	blood
2	chr13:30036000-30040400	Enhancers	Left Ventricle	heart
3	chr13:30036600-30040200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr13:30036800-30043200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr13:30038200-30041400	Enhancers	Fetal Muscle Leg	muscle
6	chr13:30038600-30040800	Enhancers	HMEC	breast
7	chr13:30038800-30041000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr13:30039000-30040600	Enhancers	Spleen	Spleen
9	chr13:30039000-30041000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr13:30039200-30040400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr13:30039200-30040600	Enhancers	K562	blood
12	chr13:30039200-30041600	Enhancers	Fetal Muscle Trunk	muscle
13	chr13:30039400-30040400	Enhancers	Right Atrium	heart
14	chr13:30039400-30040400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr13:30039400-30040600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr13:30039400-30040600	Flanking Active TSS	Fetal Heart	heart
17	chr13:30039400-30040600	Enhancers	Placenta Amnion	Placenta Amnion
18	chr13:30039400-30040600	Enhancers	Rectal Smooth Muscle	rectum
19	chr13:30039400-30040600	Enhancers	Right Ventricle	heart
20	chr13:30039600-30040200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr13:30039600-30040200	Enhancers	Ovary	ovary
22	chr13:30039600-30040400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr13:30039600-30040400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr13:30039600-30040400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr13:30039600-30040400	Enhancers	Fetal Intestine Large	intestine
26	chr13:30039600-30040400	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr13:30039600-30040400	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr13:30039600-30040600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr13:30039600-30040600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr13:30039600-30040600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr13:30039600-30040600	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr13:30039600-30040600	Enhancers	Fetal Stomach	stomach
33	chr13:30039600-30040600	Enhancers	HSMM	muscle
34	chr13:30039600-30040600	Enhancers	NH-A	brain
35	chr13:30039600-30040800	Enhancers	HSMMtube	muscle
36	chr13:30039800-30040200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr13:30039800-30040200	Enhancers	Brain Substantia Nigra	brain
38	chr13:30039800-30040200	Enhancers	Psoas Muscle	Psoas
39	chr13:30039800-30040400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr13:30039800-30040400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr13:30039800-30040400	Enhancers	Fetal Lung	lung
42	chr13:30039800-30040400	Bivalent Enhancer	Osteobl	bone
43	chr13:30039800-30040600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr13:30039800-30040600	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
45	chr13:30039800-30040600	Enhancers	NHEK	skin
46	chr13:30040000-30040200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr13:30040000-30040400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr13:30040000-30040400	Flanking Active TSS	Colon Smooth Muscle	Colon
49	chr13:30040000-30040400	Enhancers	Lung	lung
50	chr13:30040000-30040400	Enhancers	Pancreas	Pancrea

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