Variant report

Variant	rs3843490
Chromosome Location	chr5:106767522-106767523
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];0.94[ASN][1000 genomes]
rs151956	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs151958	0.92[ASN][1000 genomes]
rs152582	0.88[ASN][1000 genomes]
rs152584	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs152585	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs152587	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs152589	0.87[ASN][1000 genomes]
rs152590	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs152591	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs152592	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs152593	0.95[CHB][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs152595	0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs152596	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs152597	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs152598	0.93[ASN][1000 genomes]
rs152599	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs152601	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs152602	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs152603	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs152605	0.99[ASN][1000 genomes]
rs152606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs152607	0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs152608	1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][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];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs152613	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[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];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs154646	1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs154647	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs154648	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]
rs2283	0.81[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs252991	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs27661	0.85[CEU][hapmap];0.86[EUR][1000 genomes];0.87[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:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106751800-106767800	Weak transcription	Stomach Mucosa	stomach
2	chr5:106754000-106767600	Weak transcription	Fetal Stomach	stomach
3	chr5:106756400-106768200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:106756600-106772000	Weak transcription	Esophagus	oesophagus
5	chr5:106758600-106767800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:106758600-106767800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr5:106758600-106767800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr5:106758600-106767800	Weak transcription	Left Ventricle	heart
9	chr5:106758600-106771200	Weak transcription	Right Ventricle	heart
10	chr5:106758600-106772000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:106758600-106785000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr5:106759600-106767600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr5:106761800-106767600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:106762200-106767600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:106762200-106767600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr5:106762200-106767600	Weak transcription	HSMMtube	muscle
17	chr5:106762200-106767600	Weak transcription	NH-A	brain
18	chr5:106762200-106771600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr5:106762200-106772200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr5:106762600-106767600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:106763000-106772000	Weak transcription	Right Atrium	heart
22	chr5:106763200-106767600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr5:106763200-106767800	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr5:106763200-106773600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:106763200-106773600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:106763400-106771800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr5:106766200-106772000	Weak transcription	Brain Germinal Matrix	brain
28	chr5:106766400-106767600	Weak transcription	Fetal Lung	lung
29	chr5:106766400-106767600	Enhancers	Dnd41	blood
30	chr5:106766400-106767800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:106766400-106767800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr5:106766400-106771200	Weak transcription	Fetal Kidney	kidney
33	chr5:106766400-106775200	Weak transcription	Aorta	Aorta
34	chr5:106766600-106770400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr5:106767000-106768600	Enhancers	Muscle Satellite Cultured Cells	--
36	chr5:106767000-106768600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr5:106767200-106767600	Enhancers	Fetal Heart	heart
38	chr5:106767200-106767600	Active TSS	GM12878-XiMat	blood
39	chr5:106767200-106768000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr5:106767200-106768400	Enhancers	Hela-S3	cervix
41	chr5:106767200-106768600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:106767200-106768600	Enhancers	HMEC	breast
43	chr5:106767400-106767800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:106767400-106767800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:106767400-106767800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr5:106767400-106767800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:106767400-106767800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr5:106767400-106767800	Flanking Active TSS	NHDF-Ad	bronchial
49	chr5:106767400-106768000	Enhancers	Brain Angular Gyrus	brain
50	chr5:106767400-106768000	Flanking Active TSS	A549	lung

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