Variant report

Variant	rs163888
Chromosome Location	chr5:106889936-106889937
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11950725	1.00[ASN][1000 genomes]
rs11957374	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[ASN][1000 genomes]
rs13178589	1.00[CHB][hapmap]
rs17160159	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[ASN][1000 genomes]
rs17414033	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs1966892	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1966893	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs352605	0.96[CEU][hapmap];0.83[GIH][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes]
rs55837064	0.95[ASN][1000 genomes]
rs56195302	1.00[ASN][1000 genomes]
rs6882355	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs6883713	1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs6884705	1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs712560	0.95[ASN][1000 genomes]
rs72789671	0.95[ASN][1000 genomes]
rs72791831	1.00[ASN][1000 genomes]
rs72791834	0.88[ASN][1000 genomes]
rs7443170	0.81[ASN][1000 genomes]
rs848828	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs163888	SLC25A46	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106878800-106891600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr5:106879000-106893000	Weak transcription	Psoas Muscle	Psoas
3	chr5:106879000-106899200	Weak transcription	Fetal Stomach	stomach
4	chr5:106881600-106899600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:106883400-106890000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr5:106883800-106890200	Weak transcription	Fetal Kidney	kidney
7	chr5:106884600-106896400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:106885400-106892600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:106885600-106892800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr5:106885600-106893000	Weak transcription	Esophagus	oesophagus
11	chr5:106885600-106893200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr5:106885600-106894800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:106885600-106896400	Weak transcription	Right Atrium	heart
14	chr5:106887200-106890600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr5:106887200-106899400	Weak transcription	Fetal Lung	lung
16	chr5:106887200-106906800	Weak transcription	Right Ventricle	heart
17	chr5:106887400-106890400	Weak transcription	Adipose Nuclei	Adipose
18	chr5:106887800-106891600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:106888000-106890800	Enhancers	Muscle Satellite Cultured Cells	--
20	chr5:106889000-106890000	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr5:106889200-106890400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:106889200-106890400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:106889200-106890400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:106889200-106890400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:106889200-106890400	Weak transcription	Placenta	Placenta
26	chr5:106889200-106890400	Weak transcription	Left Ventricle	heart
27	chr5:106889200-106890400	Weak transcription	HSMMtube	muscle
28	chr5:106889200-106890600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:106889200-106890600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr5:106889200-106890800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:106889200-106892800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:106889200-106892800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:106889200-106892800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr5:106889400-106890000	Weak transcription	NHEK	skin
35	chr5:106889400-106890400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:106889400-106890400	Weak transcription	NHDF-Ad	bronchial
37	chr5:106889400-106890400	Weak transcription	Osteobl	bone
38	chr5:106889400-106890600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:106889400-106890600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr5:106889400-106890600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr5:106889400-106890600	Weak transcription	Aorta	Aorta
42	chr5:106889400-106891000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr5:106889400-106892600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr5:106889400-106892600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr5:106889400-106892600	Enhancers	A549	lung
46	chr5:106889400-106892800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr5:106889400-106892800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr5:106889400-106893000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr5:106889400-106903000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr5:106889600-106890000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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