Variant report

Variant	rs17250445
Chromosome Location	chr3:135709103-135709104
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135707339..135711075-chr3:135711449..135714009,4	MCF-7	breast:

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10512981	0.86[ASN][1000 genomes]
rs10935175	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13072596	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13097946	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13098245	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13325914	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13434196	0.86[ASN][1000 genomes]
rs1403766	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1403770	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1523595	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1523596	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1523597	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1568349	0.86[ASN][1000 genomes]
rs1568350	0.81[EUR][1000 genomes]
rs16843509	0.86[ASN][1000 genomes]
rs17196987	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17197552	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2204259	0.86[ASN][1000 genomes]
rs28449384	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28570106	0.80[EUR][1000 genomes]
rs34311570	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34409306	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34522617	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34767379	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35257855	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35722356	0.80[EUR][1000 genomes]
rs36039354	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4073308	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56807950	0.86[ASN][1000 genomes]
rs59063369	0.86[ASN][1000 genomes]
rs66544356	0.86[ASN][1000 genomes]
rs67039922	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6771224	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6771997	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6773469	0.86[ASN][1000 genomes]
rs6774289	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6779603	0.86[ASN][1000 genomes]
rs6786769	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6802139	0.86[ASN][1000 genomes]
rs6807058	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6807242	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6807565	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6809006	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6810223	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71336046	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73222222	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7427833	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7433567	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7609938	0.86[ASN][1000 genomes]
rs7621331	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7621396	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7621425	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7626676	0.86[ASN][1000 genomes]
rs7638129	0.86[ASN][1000 genomes]
rs7640153	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7641070	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7643661	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9289502	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9289503	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9808979	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9812561	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9813082	0.86[ASN][1000 genomes]
rs9814505	0.80[EUR][1000 genomes]
rs9814557	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9819440	0.80[EUR][1000 genomes]
rs9819988	0.86[ASN][1000 genomes]
rs9820189	0.80[EUR][1000 genomes]
rs9824558	0.86[ASN][1000 genomes]
rs9825239	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9826806	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9829329	0.86[ASN][1000 genomes]
rs9829476	0.86[ASN][1000 genomes]
rs9833799	0.86[ASN][1000 genomes]
rs9834104	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9836374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836758	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9837355	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9839259	0.86[ASN][1000 genomes]
rs9842840	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9842864	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9843725	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9844478	0.86[ASN][1000 genomes]
rs9846137	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9848322	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9849088	0.86[ASN][1000 genomes]
rs9851361	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9853577	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9862264	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9862743	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9862763	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9862777	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9864247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9864514	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9864656	0.86[ASN][1000 genomes]
rs9868246	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9872542	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9875328	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9876837	0.86[ASN][1000 genomes]
rs9877082	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9880721	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[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	nsv460860	chr3:135107678-135769006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv591829	chr3:135107678-135769006	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv829732	chr3:135561706-135756840	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135694000-135713600	Weak transcription	Fetal Lung	lung
2	chr3:135694000-135726600	Weak transcription	Esophagus	oesophagus
3	chr3:135694200-135709600	Weak transcription	Right Atrium	heart
4	chr3:135694200-135713400	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:135699800-135709600	Weak transcription	Right Ventricle	heart
6	chr3:135701600-135720600	Weak transcription	Ovary	ovary
7	chr3:135702200-135710200	Weak transcription	HSMMtube	muscle
8	chr3:135702600-135709800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:135702600-135710600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:135704600-135709600	Weak transcription	Psoas Muscle	Psoas
11	chr3:135704600-135716400	Weak transcription	Brain Substantia Nigra	brain
12	chr3:135704800-135709800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:135706200-135710800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:135706200-135711800	Enhancers	Muscle Satellite Cultured Cells	--
15	chr3:135706400-135711000	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr3:135706400-135711800	Enhancers	Osteobl	bone
17	chr3:135706600-135711800	Enhancers	NH-A	brain
18	chr3:135706600-135712400	Enhancers	NHDF-Ad	bronchial
19	chr3:135707000-135736400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:135707000-135741600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:135707200-135711800	Enhancers	Colon Smooth Muscle	Colon
22	chr3:135707400-135709600	Weak transcription	Aorta	Aorta
23	chr3:135707600-135711800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:135707600-135711800	Enhancers	NHLF	lung
25	chr3:135707800-135710200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:135707800-135711600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:135708000-135710800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:135708000-135711800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:135708200-135709400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:135708200-135709600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:135708200-135710400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:135708200-135716600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr3:135708200-135730200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:135708600-135709600	Weak transcription	HMEC	breast
35	chr3:135708600-135709600	Weak transcription	NHEK	skin
36	chr3:135708600-135713600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:135708800-135709400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:135708800-135709800	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr3:135709000-135709800	Weak transcription	HSMM	muscle
40	chr3:135709000-135710000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:135709000-135710000	Enhancers	Left Ventricle	heart
42	chr3:135709000-135711400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:135709000-135712000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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