Variant report

Variant	rs73192754
Chromosome Location	chr3:105244693-105244694
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	chr3:105235908..105237655-chr3:105242173..105244710,2	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs11710166	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11710857	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11713535	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11714275	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11714277	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11715283	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11716035	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11718405	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11718457	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11719817	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1898655	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1955135	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2200473	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2399049	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2895300	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34029528	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3772542	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772544	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772547	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs481177	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526297	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57986655	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59322590	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs598425	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61522255	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6771935	0.85[ASN][1000 genomes]
rs6771987	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6786815	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6794273	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73175407	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73175433	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73175435	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73175442	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73175449	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73175451	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73175463	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73175491	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73177465	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73177470	0.85[ASN][1000 genomes]
rs73177478	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73177489	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73177494	0.85[ASN][1000 genomes]
rs73179378	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73179384	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73181374	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73181376	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73181380	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73181387	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73181395	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73181396	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73181397	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73181401	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73183103	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73183108	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73183112	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73183114	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73183115	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73183185	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73183186	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73183187	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73183188	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73183198	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73185106	0.80[EUR][1000 genomes]
rs73185114	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73185115	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73189021	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73189028	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73189034	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73189060	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73192717	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73192730	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192733	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192737	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73192770	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs978436	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv829651	chr3:105203424-105402136	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv460811	chr3:105212993-105316769	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv591240	chr3:105212993-105316769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105221400-105300400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:105222200-105260600	Weak transcription	Fetal Kidney	kidney
3	chr3:105222800-105246000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:105223800-105274800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:105229600-105260400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:105230200-105262600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:105232200-105245400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:105232200-105245400	Weak transcription	NHEK	skin
9	chr3:105232200-105245600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:105232200-105274000	Weak transcription	HSMMtube	muscle
11	chr3:105233400-105250600	Weak transcription	HSMM	muscle
12	chr3:105234200-105260400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:105234600-105260600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:105234600-105261000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:105234600-105274600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:105236200-105251000	Weak transcription	Aorta	Aorta
17	chr3:105236400-105245200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:105236400-105251000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:105237800-105251000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:105237800-105259000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:105237800-105274600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:105237800-105275800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr3:105239400-105248000	Weak transcription	HUVEC	blood vessel
24	chr3:105240000-105252400	Weak transcription	Gastric	stomach
25	chr3:105241000-105260400	Weak transcription	Pancreas	Pancrea
26	chr3:105241200-105250600	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr3:105241600-105250800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:105241600-105260200	Weak transcription	HepG2	liver
29	chr3:105241800-105259000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr3:105242000-105259800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr3:105242000-105293600	Weak transcription	Lung	lung
32	chr3:105242200-105252800	Weak transcription	Fetal Intestine Large	intestine
33	chr3:105242200-105259000	Weak transcription	Ovary	ovary
34	chr3:105242400-105245200	Enhancers	Brain Hippocampus Middle	brain
35	chr3:105242400-105256400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:105242400-105280400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr3:105242600-105245400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:105242800-105245600	Weak transcription	A549	lung
39	chr3:105242800-105245600	Weak transcription	NHDF-Ad	bronchial
40	chr3:105242800-105266800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr3:105243000-105245400	Strong transcription	Primary B cells from peripheral blood	blood
42	chr3:105243000-105245600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:105243200-105245000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:105243200-105245000	Strong transcription	Primary B cells from cord blood	blood
45	chr3:105243200-105245000	Strong transcription	NHLF	lung
46	chr3:105243200-105245200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:105243200-105245400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:105243200-105245800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr3:105243200-105246400	Strong transcription	GM12878-XiMat	blood
50	chr3:105243200-105248400	Enhancers	Brain Cingulate Gyrus	brain

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