Variant report

Variant	rs3797517
Chromosome Location	chr5:106738959-106738960
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10085055	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11242636	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11956440	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13178242	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13182976	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1835111	0.86[TSI][hapmap]
rs1975009	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28683545	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34366978	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34583348	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35021422	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3756544	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3776792	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3797510	1.00[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes]
rs3797513	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3797514	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3797516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3797521	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3797527	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3822565	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3873122	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3873123	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3901010	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs3909931	0.86[TSI][hapmap]
rs58696640	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59863014	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs66505151	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6868410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72785812	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72785815	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72785818	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72785829	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7703776	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030118	chr5:106006097-106847949	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1034276	chr5:106461538-106944163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537851	chr5:106461538-106944163	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv34018	chr5:106720912-107110506	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv820161	chr5:106737870-106739081	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	n/a	n/a	inside rSNPs	n/a

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106720400-106740800	Weak transcription	Aorta	Aorta
2	chr5:106725800-106740400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:106732200-106739400	Weak transcription	GM12878-XiMat	blood
4	chr5:106732200-106753200	Weak transcription	Fetal Kidney	kidney
5	chr5:106733600-106744800	Weak transcription	Right Ventricle	heart
6	chr5:106735200-106741200	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr5:106735200-106741400	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr5:106736000-106740000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:106736000-106740000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:106736200-106742200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr5:106736400-106740200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:106736400-106741200	Enhancers	A549	lung
13	chr5:106736600-106740600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr5:106736800-106740000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:106736800-106740200	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr5:106737200-106739600	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr5:106737200-106740000	Enhancers	Brain Germinal Matrix	brain
18	chr5:106737400-106739200	Enhancers	Fetal Brain Male	brain
19	chr5:106737400-106739600	Enhancers	Brain Anterior Caudate	brain
20	chr5:106737400-106740400	Enhancers	HMEC	breast
21	chr5:106737400-106741400	Enhancers	Fetal Heart	heart
22	chr5:106737600-106739200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:106737600-106740800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr5:106737800-106739000	Enhancers	H1 Cell Line	embryonic stem cell
25	chr5:106737800-106739000	Enhancers	Placenta Amnion	Placenta Amnion
26	chr5:106737800-106739600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr5:106738000-106740200	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr5:106738200-106739000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:106738200-106739000	Enhancers	H9 Cell Line	embryonic stem cell
30	chr5:106738200-106739000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr5:106738200-106739000	Enhancers	Brain Cingulate Gyrus	brain
32	chr5:106738200-106739000	Enhancers	Ovary	ovary
33	chr5:106738200-106739600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr5:106738200-106739600	Enhancers	Muscle Satellite Cultured Cells	--
35	chr5:106738200-106739800	Enhancers	HSMM	muscle
36	chr5:106738200-106740800	Enhancers	NHEK	skin
37	chr5:106738200-106741200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:106738400-106739000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr5:106738400-106739000	Enhancers	Left Ventricle	heart
40	chr5:106738400-106739600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:106738400-106739600	Enhancers	Fetal Lung	lung
42	chr5:106738600-106739000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr5:106738600-106739000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr5:106738600-106739000	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr5:106738600-106739000	Enhancers	Right Atrium	heart
46	chr5:106738600-106739000	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr5:106738600-106739400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr5:106738600-106739400	Enhancers	Osteobl	bone
49	chr5:106738800-106739000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
50	chr5:106738800-106739000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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