Variant report

Variant	rs1720828
Chromosome Location	chr3:138103422-138103423
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1092338	0.80[ASN][1000 genomes]
rs1199329	1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1199330	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1199332	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1199337	1.00[CHB][hapmap]
rs1199338	1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[ASN][1000 genomes]
rs1199340	0.98[ASN][1000 genomes]
rs13324341	0.89[CHB][hapmap];0.90[CHD][hapmap];0.86[LWK][hapmap];0.91[YRI][hapmap]
rs1678440	0.81[ASN][1000 genomes]
rs1678442	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1678443	1.00[CHB][hapmap];0.99[ASN][1000 genomes]
rs1720819	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs1720823	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs181877	0.82[ASN][1000 genomes]
rs185244	0.81[ASN][1000 genomes]
rs1871398	1.00[EUR][1000 genomes]
rs2054468	0.80[CHD][hapmap]
rs253661	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs253663	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs253665	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs253667	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3773752	0.87[CHD][hapmap]
rs3773757	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs40593	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4678260	0.90[CHD][hapmap]
rs4678409	0.80[CHD][hapmap]
rs4678415	0.90[CHD][hapmap]
rs6782181	1.00[CHD][hapmap]
rs6789235	0.89[CHB][hapmap]
rs6807945	0.89[CHB][hapmap];0.87[CHD][hapmap];0.86[LWK][hapmap]
rs72630192	1.00[EUR][1000 genomes]
rs730158	0.90[CHD][hapmap]
rs731632	0.90[CHD][hapmap]
rs751357	0.90[CHD][hapmap]
rs774009	1.00[CHB][hapmap];0.87[JPT][hapmap];0.99[ASN][1000 genomes]
rs774013	0.86[EUR][1000 genomes]
rs796493	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9289559	0.90[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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

No data

Chromatin state (count:62 , 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	chr3:138094000-138104800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:138097600-138116000	Weak transcription	Aorta	Aorta
6	chr3:138097600-138116600	Weak transcription	Brain Germinal Matrix	brain
7	chr3:138098200-138104200	Enhancers	Fetal Heart	heart
8	chr3:138098400-138103800	Enhancers	Brain Substantia Nigra	brain
9	chr3:138099200-138104000	Enhancers	Right Ventricle	heart
10	chr3:138099600-138105200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr3:138099800-138103800	Enhancers	Adipose Nuclei	Adipose
12	chr3:138099800-138103800	Enhancers	Brain Anterior Caudate	brain
13	chr3:138099800-138103800	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr3:138099800-138103800	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr3:138099800-138104000	Enhancers	Left Ventricle	heart
16	chr3:138099800-138104200	Enhancers	Placenta	Placenta
17	chr3:138099800-138104200	Enhancers	Right Atrium	heart
18	chr3:138100000-138103600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:138100000-138103800	Enhancers	Brain Angular Gyrus	brain
20	chr3:138100000-138103800	Enhancers	Brain Cingulate Gyrus	brain
21	chr3:138100000-138104000	Genic enhancers	HSMMtube	muscle
22	chr3:138101200-138105000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:138101200-138106000	Weak transcription	Fetal Stomach	stomach
24	chr3:138101200-138115000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:138101400-138106400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:138101400-138108000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr3:138101400-138108400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:138101400-138123000	Weak transcription	Fetal Lung	lung
29	chr3:138101600-138103600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:138101600-138104200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr3:138101600-138107800	Weak transcription	Osteobl	bone
32	chr3:138101600-138108000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:138101600-138108200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:138101600-138108200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:138101600-138108200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:138101600-138120400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:138101800-138108000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:138101800-138108200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:138101800-138108200	Weak transcription	Pancreas	Pancrea
40	chr3:138101800-138108400	Weak transcription	Fetal Muscle Leg	muscle
41	chr3:138101800-138108400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr3:138101800-138108600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:138102000-138107000	Strong transcription	HSMM	muscle
44	chr3:138102000-138108200	Weak transcription	Esophagus	oesophagus
45	chr3:138102000-138108200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr3:138102200-138105200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:138102200-138106600	Weak transcription	Fetal Brain Female	brain
48	chr3:138102400-138103800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:138102400-138108000	Weak transcription	Psoas Muscle	Psoas
50	chr3:138102600-138103600	Enhancers	HMEC	breast

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