Variant report

Variant	rs162429
Chromosome Location	chr3:78936401-78936402
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs13075210	0.83[CHB][hapmap]
rs1355983	0.81[CHB][hapmap]
rs1487135	0.87[CHB][hapmap]
rs162262	0.96[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs162263	0.87[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.80[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs162264	0.93[CHB][hapmap];0.80[EUR][1000 genomes]
rs162265	0.92[CHB][hapmap];0.82[EUR][1000 genomes]
rs162266	0.85[EUR][1000 genomes]
rs162267	0.85[EUR][1000 genomes]
rs162268	0.93[CHB][hapmap];0.80[CHD][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs162423	0.87[CHB][hapmap]
rs162425	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[EUR][1000 genomes]
rs162426	0.95[EUR][1000 genomes]
rs162427	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs162428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17311057	0.85[CHB][hapmap]
rs17311169	0.87[CHB][hapmap]
rs17313732	0.81[CHB][hapmap]
rs1825760	0.87[CHB][hapmap]
rs1865861	0.80[CHB][hapmap]
rs1865863	0.80[CHB][hapmap]
rs186648	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs186688	0.93[CHB][hapmap];0.81[EUR][1000 genomes]
rs2018432	0.87[CHB][hapmap]
rs2082973	0.87[CHB][hapmap]
rs328045	0.87[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs328047	0.93[CHB][hapmap];0.93[CHD][hapmap];0.93[MEX][hapmap];0.80[TSI][hapmap]
rs329805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs329811	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs329812	0.95[CEU][hapmap];0.87[CHB][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs329813	0.91[CEU][hapmap];0.93[CHB][hapmap];0.80[JPT][hapmap]
rs329814	0.93[CHB][hapmap];0.82[CHD][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs329815	0.86[EUR][1000 genomes]
rs329816	0.93[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs329817	0.86[EUR][1000 genomes]
rs329818	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs329819	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs329820	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs329821	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs329822	0.93[CHB][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs329824	0.95[EUR][1000 genomes]
rs329825	0.92[CHB][hapmap];0.81[EUR][1000 genomes]
rs331134	0.84[CHB][hapmap]
rs331139	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs331143	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs331145	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs331149	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs331158	0.91[CEU][hapmap];0.93[CHB][hapmap]
rs331161	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs331162	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs331163	0.85[EUR][1000 genomes]
rs331164	0.89[EUR][1000 genomes]
rs331181	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs331182	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs331183	0.82[EUR][1000 genomes]
rs331184	0.86[EUR][1000 genomes]
rs331188	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs331189	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs331190	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs331199	0.83[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs333483	0.86[CHB][hapmap]
rs333493	0.87[CHB][hapmap]
rs333507	0.87[CHB][hapmap]
rs369346	0.93[CHB][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs379346	0.93[CHB][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs387900	0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs388421	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs409361	0.83[EUR][1000 genomes]
rs420481	0.82[EUR][1000 genomes]
rs425121	0.83[EUR][1000 genomes]
rs432141	0.94[EUR][1000 genomes]
rs434929	0.83[EUR][1000 genomes]
rs453354	0.86[EUR][1000 genomes]
rs4681013	0.90[CEU][hapmap];0.92[CHB][hapmap]
rs479956	0.87[CEU][hapmap];0.93[CHB][hapmap];0.83[EUR][1000 genomes]
rs484531	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs498805	0.87[CEU][hapmap];0.93[CHB][hapmap];0.93[MEX][hapmap];0.83[EUR][1000 genomes]
rs512135	0.83[EUR][1000 genomes]
rs531125	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[EUR][1000 genomes]
rs6548600	0.84[CHB][hapmap]
rs6548601	0.93[CHB][hapmap]
rs6770452	0.87[CHB][hapmap]
rs6772919	0.93[CHB][hapmap]
rs6800782	0.87[CEU][hapmap];0.93[CHB][hapmap];0.85[EUR][1000 genomes]
rs7610996	0.87[CHB][hapmap]
rs7617433	0.86[CHB][hapmap]
rs7617538	0.83[CEU][hapmap];0.93[CHB][hapmap]
rs7619765	0.83[EUR][1000 genomes]
rs7629522	0.87[CHB][hapmap]
rs7650002	0.87[CHB][hapmap]
rs9866912	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv834744	chr3:78911545-79076470	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv877020	chr3:78913203-78975982	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv470672	chr3:78913203-78985805	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv590734	chr3:78915205-78985805	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv590735	chr3:78922852-78977507	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78921600-78936600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:78922600-78944000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:78923000-78943800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:78927600-78943800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:78930400-78937800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:78930400-78938600	Weak transcription	Psoas Muscle	Psoas
7	chr3:78930400-78942200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:78930400-78944000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:78930600-78948600	Weak transcription	Fetal Lung	lung
10	chr3:78930800-78936800	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:78930800-78943800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:78931600-78937200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:78935400-78939200	Enhancers	Fetal Brain Male	brain
14	chr3:78935800-78936800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:78936000-78936800	Enhancers	NHEK	skin
16	chr3:78936000-78937000	Enhancers	NH-A	brain
17	chr3:78936000-78937400	Enhancers	HSMM	muscle
18	chr3:78936000-78938400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr3:78936200-78936800	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr3:78936200-78937000	Enhancers	Osteobl	bone
21	chr3:78936200-78937400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:78936200-78937400	Enhancers	HMEC	breast
23	chr3:78936200-78938000	Enhancers	NHLF	lung
24	chr3:78936200-78938200	Enhancers	HepG2	liver
25	chr3:78936400-78936600	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr3:78936400-78936600	Flanking Active TSS	A549	lung
27	chr3:78936400-78936600	Enhancers	NHDF-Ad	bronchial
28	chr3:78936400-78936800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:78936400-78936800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:78936400-78936800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr3:78936400-78937000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:78936400-78937000	Enhancers	Fetal Brain Female	brain
33	chr3:78936400-78937000	Enhancers	HSMMtube	muscle
34	chr3:78936400-78937200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:78936400-78937400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:78936400-78937800	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr3:78936400-78937800	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr3:78936400-78938600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:78936400-78938800	Enhancers	Brain Angular Gyrus	brain
40	chr3:78936400-78938800	Enhancers	Brain Hippocampus Middle	brain

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