Variant report

Variant	rs252991
Chromosome Location	chr5:106767346-106767347
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs151956	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs152584	0.85[EUR][1000 genomes]
rs152585	0.86[EUR][1000 genomes]
rs152587	1.00[CEU][hapmap];0.88[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs152590	0.88[EUR][1000 genomes]
rs152595	0.88[GIH][hapmap]
rs152596	0.88[GIH][hapmap]
rs152597	0.94[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs152599	0.83[GIH][hapmap];0.87[JPT][hapmap]
rs152601	0.86[JPT][hapmap]
rs152602	0.88[CEU][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs152603	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs152606	1.00[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs152608	0.90[GIH][hapmap];0.87[JPT][hapmap]
rs152609	0.86[JPT][hapmap]
rs152611	0.86[JPT][hapmap]
rs152612	0.83[CEU][hapmap];0.85[JPT][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs152613	1.00[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs154645	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs154646	0.90[GIH][hapmap];0.87[JPT][hapmap]
rs154647	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs154648	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]
rs2283	0.81[ASW][hapmap];0.88[CEU][hapmap];0.97[GIH][hapmap];0.80[MKK][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs27661	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs3843490	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]

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	chr5:106762600-106767400	Weak transcription	NHEK	skin
21	chr5:106762600-106767600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:106762800-106767400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:106763000-106767400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:106763000-106772000	Weak transcription	Right Atrium	heart
25	chr5:106763200-106767600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr5:106763200-106767800	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr5:106763200-106773600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:106763200-106773600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:106763400-106771800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr5:106765600-106767400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:106766000-106767400	Weak transcription	Osteobl	bone
32	chr5:106766200-106767400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:106766200-106772000	Weak transcription	Brain Germinal Matrix	brain
34	chr5:106766400-106767400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:106766400-106767400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr5:106766400-106767400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:106766400-106767400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:106766400-106767400	Weak transcription	HSMM	muscle
39	chr5:106766400-106767400	Weak transcription	HUVEC	blood vessel
40	chr5:106766400-106767400	Weak transcription	NHLF	lung
41	chr5:106766400-106767600	Weak transcription	Fetal Lung	lung
42	chr5:106766400-106767600	Enhancers	Dnd41	blood
43	chr5:106766400-106767800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr5:106766400-106767800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr5:106766400-106771200	Weak transcription	Fetal Kidney	kidney
46	chr5:106766400-106775200	Weak transcription	Aorta	Aorta
47	chr5:106766600-106770400	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr5:106767000-106767400	Enhancers	NHDF-Ad	bronchial
49	chr5:106767000-106768600	Enhancers	Muscle Satellite Cultured Cells	--
50	chr5:106767000-106768600	Enhancers	Cortex derived primary cultured neurospheres	brain

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