Variant report

Variant	rs12522862
Chromosome Location	chr5:112568979-112568980
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10428666	0.84[EUR][1000 genomes]
rs10519343	1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10519345	0.82[YRI][hapmap]
rs10519346	1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1116547	0.90[MEX][hapmap]
rs11241197	0.92[EUR][1000 genomes]
rs11241201	0.90[MEX][hapmap]
rs11241206	0.85[MEX][hapmap]
rs11738215	0.85[MEX][hapmap]
rs11740190	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11740233	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11740318	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11740353	1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11740443	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11741794	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11741937	0.89[EUR][1000 genomes]
rs11743767	1.00[CEU][hapmap]
rs11746532	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11746791	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11748058	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11748465	1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11748503	0.84[EUR][1000 genomes]
rs11748524	1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11749864	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12186466	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12188069	1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12188070	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12188230	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12521391	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12522683	1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12523027	0.92[EUR][1000 genomes]
rs12523284	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17135454	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17135463	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17135506	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17135507	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17135514	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17135515	1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17135517	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17135519	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17135520	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17135526	1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17135531	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17135534	0.90[MEX][hapmap]
rs17135546	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17164185	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1845289	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1850410	0.89[EUR][1000 genomes]
rs1850411	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1997521	1.00[CHD][hapmap];0.90[MEX][hapmap]
rs2068923	1.00[GIH][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs2091803	0.82[CHD][hapmap]
rs34271294	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4632792	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4705549	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4705810	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56294433	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60437559	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6594695	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6594696	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6594697	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6864528	0.85[MEX][hapmap]
rs6877524	0.83[GIH][hapmap];0.90[MEX][hapmap]
rs6879761	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6887565	1.00[CHD][hapmap];0.90[MEX][hapmap]
rs73244759	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73244767	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73244768	0.85[ASN][1000 genomes]
rs73244769	0.80[ASN][1000 genomes]
rs73244770	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73244772	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73246604	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73246629	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73246681	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7703865	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs971370	1.00[CHD][hapmap];0.90[MEX][hapmap]
rs971371	1.00[CHD][hapmap];0.90[MEX][hapmap]
rs977997	1.00[CHD][hapmap];0.90[MEX][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	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 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	chr5:112548400-112581800	Weak transcription	Fetal Kidney	kidney
2	chr5:112557200-112585800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:112559000-112570000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:112559000-112571200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:112560800-112569000	Weak transcription	Osteobl	bone
6	chr5:112561200-112570400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:112561600-112575000	Weak transcription	Right Ventricle	heart
8	chr5:112562200-112570400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:112565400-112572000	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr5:112566200-112572400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:112566400-112569000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:112566400-112569200	Enhancers	HMEC	breast
13	chr5:112566400-112569600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:112566400-112569800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr5:112566400-112571000	Enhancers	Adipose Nuclei	Adipose
16	chr5:112566400-112571200	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr5:112566400-112572400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:112566400-112574000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:112566600-112569400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr5:112566800-112569000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr5:112566800-112570600	Enhancers	NHDF-Ad	bronchial
22	chr5:112567000-112569200	Enhancers	HUVEC	blood vessel
23	chr5:112567000-112569400	Enhancers	Colon Smooth Muscle	Colon
24	chr5:112567200-112569800	Enhancers	NH-A	brain
25	chr5:112567200-112571000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr5:112567200-112572400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:112567200-112572400	Enhancers	NHEK	skin
28	chr5:112567400-112569800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr5:112567400-112570000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:112567400-112571200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr5:112567400-112572800	Enhancers	Stomach Mucosa	stomach
32	chr5:112567400-112573200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr5:112567800-112569400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:112567800-112569400	Enhancers	Liver	Liver
35	chr5:112567800-112569800	Enhancers	Fetal Heart	heart
36	chr5:112567800-112570800	Enhancers	Ovary	ovary
37	chr5:112568000-112569000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr5:112568000-112569000	Enhancers	Small Intestine	intestine
39	chr5:112568000-112569600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr5:112568000-112569600	Enhancers	Fetal Brain Male	brain
41	chr5:112568000-112569800	Enhancers	Fetal Lung	lung
42	chr5:112568000-112569800	Enhancers	HSMMtube	muscle
43	chr5:112568000-112571000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr5:112568200-112569400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr5:112568200-112570600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr5:112568400-112572400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:112568600-112569400	Weak transcription	Fetal Stomach	stomach
48	chr5:112568600-112569600	Weak transcription	HSMM	muscle
49	chr5:112568600-112575000	Weak transcription	Left Ventricle	heart
50	chr5:112568800-112569000	Enhancers	Skeletal Muscle Female	skeletal muscle

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