Variant report

Variant	rs169406
Chromosome Location	chr5:70946113-70946114
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs157192	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs157193	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs166758	0.84[CEU][hapmap];0.87[CHB][hapmap];0.96[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs182191	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277927	0.83[EUR][1000 genomes]
rs277935	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs277941	0.81[AMR][1000 genomes]
rs277952	0.84[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs277955	0.84[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs277975	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277982	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs277983	0.84[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs277984	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs277987	0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs277988	0.84[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs277990	0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs277991	0.83[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs277992	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs277993	0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs277994	0.84[CEU][hapmap];0.80[AMR][1000 genomes]
rs277998	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs282357	0.84[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs368462	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs388918	0.81[AMR][1000 genomes]
rs412766	0.91[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs457889	0.81[AMR][1000 genomes]
rs458829	0.81[AMR][1000 genomes]
rs461690	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs461942	0.81[AMR][1000 genomes]
rs462534	0.81[AMR][1000 genomes]
rs464639	0.81[AMR][1000 genomes]
rs467880	0.81[AMR][1000 genomes]
rs467883	0.81[AMR][1000 genomes]
rs468010	0.81[AMR][1000 genomes]
rs468796	0.81[AMR][1000 genomes]
rs617876	0.81[AMR][1000 genomes]

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	nsv1034703	chr5:70391173-70995695	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	28 gene(s)	inside rSNPs	diseases
2	nsv830340	chr5:70797113-70967110	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv532805	chr5:70916228-71020967	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70898400-70955000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr5:70898600-70948400	Weak transcription	Brain Germinal Matrix	brain
3	chr5:70906600-70952400	Weak transcription	Stomach Mucosa	stomach
4	chr5:70914200-70948800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:70915400-70950800	Weak transcription	NHLF	lung
6	chr5:70919800-70955000	Weak transcription	HUVEC	blood vessel
7	chr5:70925400-70950600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:70926600-70954000	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr5:70927000-70954000	Strong transcription	Dnd41	blood
10	chr5:70927000-70954200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:70930400-70952600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr5:70931400-70953600	Weak transcription	HSMM	muscle
13	chr5:70931600-70947000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr5:70933400-70946200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr5:70934800-70953800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:70935000-70955800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr5:70935400-70947600	Weak transcription	Fetal Brain Male	brain
18	chr5:70935600-70948600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr5:70936600-70955200	Weak transcription	Fetal Heart	heart
20	chr5:70937000-70947000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:70938000-70947000	Weak transcription	NHDF-Ad	bronchial
22	chr5:70938400-70954000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr5:70938600-70948400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:70938800-70947200	Weak transcription	Pancreas	Pancrea
25	chr5:70938800-70948200	Weak transcription	Fetal Brain Female	brain
26	chr5:70939400-70948600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:70940800-70954600	Strong transcription	Liver	Liver
28	chr5:70941000-70950000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr5:70941000-70951400	Strong transcription	Fetal Intestine Large	intestine
30	chr5:70941200-70955000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr5:70941400-70946400	Strong transcription	Primary T cells from cord blood	blood
32	chr5:70941400-70946400	Strong transcription	GM12878-XiMat	blood
33	chr5:70941400-70947200	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr5:70941400-70950000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr5:70941400-70950000	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr5:70941400-70950200	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr5:70941400-70954200	Strong transcription	Placenta	Placenta
38	chr5:70941400-70954400	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr5:70941400-70954400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr5:70941400-70954600	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr5:70941400-70954600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr5:70941600-70948800	Strong transcription	Left Ventricle	heart
43	chr5:70941600-70949000	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr5:70941600-70954400	Strong transcription	Duodenum Mucosa	Duodenum
45	chr5:70941600-70954600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr5:70942000-70946200	Strong transcription	Brain Anterior Caudate	brain
47	chr5:70942000-70948800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr5:70942000-70949400	Strong transcription	HepG2	liver
49	chr5:70942000-70949800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:70942000-70950000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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