Variant report

Variant	rs154648
Chromosome Location	chr5:106767937-106767938
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs115779	0.90[ASN][1000 genomes]
rs149444	0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs149498	0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs151956	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs151958	0.91[ASN][1000 genomes]
rs152582	0.87[ASN][1000 genomes]
rs152584	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs152585	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs152587	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs152589	0.86[ASN][1000 genomes]
rs152590	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs152591	1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs152592	1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs152593	0.95[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs152595	0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs152596	1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.92[ASN][1000 genomes]
rs152597	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];0.84[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs152598	0.92[ASN][1000 genomes]
rs152599	1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs152601	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs152602	0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs152603	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs152605	0.99[ASN][1000 genomes]
rs152606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs152607	0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs152608	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.99[ASN][1000 genomes]
rs152609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs152611	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs152612	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs152613	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs153686	0.94[ASN][1000 genomes]
rs154645	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs154646	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.99[ASN][1000 genomes]
rs154647	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2283	0.81[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs252991	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.98[LWK][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs27661	0.85[CEU][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3843490	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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	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

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106756400-106768200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr5:106756600-106772000	Weak transcription	Esophagus	oesophagus
3	chr5:106758600-106771200	Weak transcription	Right Ventricle	heart
4	chr5:106758600-106772000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:106758600-106785000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr5:106762200-106771600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:106762200-106772200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:106763000-106772000	Weak transcription	Right Atrium	heart
9	chr5:106763200-106773600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:106763200-106773600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:106763400-106771800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr5:106766200-106772000	Weak transcription	Brain Germinal Matrix	brain
13	chr5:106766400-106771200	Weak transcription	Fetal Kidney	kidney
14	chr5:106766400-106775200	Weak transcription	Aorta	Aorta
15	chr5:106766600-106770400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr5:106767000-106768600	Enhancers	Muscle Satellite Cultured Cells	--
17	chr5:106767000-106768600	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr5:106767200-106768000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:106767200-106768400	Enhancers	Hela-S3	cervix
20	chr5:106767200-106768600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:106767200-106768600	Enhancers	HMEC	breast
22	chr5:106767400-106768000	Enhancers	Brain Angular Gyrus	brain
23	chr5:106767400-106768000	Flanking Active TSS	A549	lung
24	chr5:106767400-106768200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:106767400-106768400	Enhancers	Osteobl	bone
26	chr5:106767400-106768600	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr5:106767400-106768600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:106767400-106768600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:106767400-106768600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:106767400-106768600	Enhancers	HSMM	muscle
31	chr5:106767400-106768600	Enhancers	HUVEC	blood vessel
32	chr5:106767400-106768600	Enhancers	NHEK	skin
33	chr5:106767400-106768600	Enhancers	NHLF	lung
34	chr5:106767600-106768200	Enhancers	Placenta Amnion	Placenta Amnion
35	chr5:106767600-106768200	Enhancers	NH-A	brain
36	chr5:106767600-106768600	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr5:106767600-106768600	Flanking Active TSS	Fetal Heart	heart
38	chr5:106767600-106768600	Enhancers	Fetal Lung	lung
39	chr5:106767600-106768600	Enhancers	HSMMtube	muscle
40	chr5:106767800-106768000	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr5:106767800-106768000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr5:106767800-106768000	Enhancers	Left Ventricle	heart
43	chr5:106767800-106768000	Active TSS	GM12878-XiMat	blood
44	chr5:106767800-106768200	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr5:106767800-106768200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr5:106767800-106768200	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr5:106767800-106768200	Weak transcription	Fetal Stomach	stomach
48	chr5:106767800-106768400	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr5:106767800-106768400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr5:106767800-106768400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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