Variant report

Variant	rs1720825
Chromosome Location	chr3:138108083-138108084
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	chr3:138108024..138110952-chr3:138113271..138115084,3	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1199328	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1199333	0.89[CEU][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1199334	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs1199335	0.90[CEU][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1199336	0.89[CEU][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1199346	0.80[AMR][1000 genomes]
rs1199347	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1201763	0.80[AMR][1000 genomes]
rs1209710	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1212469	0.95[EUR][1000 genomes]
rs13082471	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1308362	0.95[CEU][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1624314	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs166195	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs166196	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1679149	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1720827	1.00[ASN][1000 genomes]
rs183151	0.90[EUR][1000 genomes]
rs194146	0.91[EUR][1000 genomes]
rs253662	0.95[CEU][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs253664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs253666	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs42761	0.80[AMR][1000 genomes]
rs4346503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4437085	0.83[YRI][hapmap];0.80[AMR][1000 genomes]
rs4678416	0.92[EUR][1000 genomes]
rs6809480	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs774373	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs799328	0.89[CEU][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs808934	1.00[ASN][1000 genomes]
rs811332	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv528349	chr3:138025396-138132393	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1796956	chr3:138051423-138122781	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv1848610	chr3:138051423-138133412	Bivalent Enhancer Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv1797142	chr3:138087467-138122781	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv1845560	chr3:138087467-138133412	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv3447663	chr3:138096329-138273034	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv460864	chr3:138100539-138194435	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv591853	chr3:138100539-138194435	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
12	nsv526089	chr3:138106698-138122781	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138076000-138108200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:138081600-138108200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:138090400-138119400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:138097600-138116000	Weak transcription	Aorta	Aorta
5	chr3:138097600-138116600	Weak transcription	Brain Germinal Matrix	brain
6	chr3:138101200-138115000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:138101400-138108400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:138101400-138123000	Weak transcription	Fetal Lung	lung
9	chr3:138101600-138108200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:138101600-138108200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:138101600-138108200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:138101600-138120400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:138101800-138108200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:138101800-138108200	Weak transcription	Pancreas	Pancrea
15	chr3:138101800-138108400	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:138101800-138108400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:138101800-138108600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:138102000-138108200	Weak transcription	Esophagus	oesophagus
19	chr3:138102000-138108200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:138102600-138108200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:138102600-138109200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:138103400-138108600	Weak transcription	NHEK	skin
23	chr3:138103600-138108200	Weak transcription	HMEC	breast
24	chr3:138103800-138108200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:138103800-138108200	Weak transcription	Lung	lung
26	chr3:138103800-138108600	Weak transcription	Brain Angular Gyrus	brain
27	chr3:138103800-138109200	Weak transcription	Brain Substantia Nigra	brain
28	chr3:138105200-138109000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:138105400-138108400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:138106000-138108400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:138106000-138109400	Enhancers	Left Ventricle	heart
32	chr3:138106200-138108800	Weak transcription	Fetal Stomach	stomach
33	chr3:138106200-138109800	Enhancers	Adipose Nuclei	Adipose
34	chr3:138107000-138108200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr3:138107000-138108400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:138107200-138108600	Weak transcription	Fetal Brain Female	brain
37	chr3:138107400-138109800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:138107600-138109600	Enhancers	Brain Anterior Caudate	brain
39	chr3:138107600-138112000	Enhancers	Fetal Heart	heart
40	chr3:138107800-138108600	Enhancers	Osteobl	bone
41	chr3:138107800-138109200	Enhancers	Right Ventricle	heart
42	chr3:138107800-138110200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:138108000-138108400	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr3:138108000-138108400	Enhancers	HSMM	muscle
45	chr3:138108000-138108400	Genic enhancers	HSMMtube	muscle
46	chr3:138108000-138108600	Enhancers	Muscle Satellite Cultured Cells	--
47	chr3:138108000-138108600	Enhancers	NH-A	brain
48	chr3:138108000-138108800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:138108000-138108800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:138108000-138109000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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