Variant report

Variant	rs329824
Chromosome Location	chr3:78945698-78945699
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:78944946..78946715-chr3:79016289..79018203,2	MCF-7	breast:
2	chr3:78944908..78947442-chr3:78948328..78949927,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs13075210	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs162262	0.85[EUR][1000 genomes]
rs162263	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs162264	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs162265	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs162266	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs162267	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs162268	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs162425	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs162426	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs162427	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs162428	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs162429	0.95[EUR][1000 genomes]
rs186648	0.86[EUR][1000 genomes]
rs186688	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs328045	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs329805	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs329811	0.85[EUR][1000 genomes]
rs329812	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs329814	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs329815	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs329816	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs329817	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs329818	0.91[EUR][1000 genomes]
rs329819	0.89[EUR][1000 genomes]
rs329820	0.83[EUR][1000 genomes]
rs329821	0.85[EUR][1000 genomes]
rs329822	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs329825	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs331139	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs331143	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs331145	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs331149	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs331161	0.86[EUR][1000 genomes]
rs331162	0.87[EUR][1000 genomes]
rs331163	0.87[EUR][1000 genomes]
rs331164	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs331181	0.89[EUR][1000 genomes]
rs331182	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs331183	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs331184	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs331188	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs331189	0.89[EUR][1000 genomes]
rs331190	0.87[EUR][1000 genomes]
rs331199	0.85[EUR][1000 genomes]
rs369346	0.81[EUR][1000 genomes]
rs379346	0.80[EUR][1000 genomes]
rs388421	0.82[EUR][1000 genomes]
rs409361	0.84[EUR][1000 genomes]
rs420481	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs425121	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs432141	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs434929	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs453354	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs479956	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs484531	0.81[EUR][1000 genomes]
rs498805	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs512135	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs531125	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6800782	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7617538	0.85[ASN][1000 genomes]
rs7619765	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]

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:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78930600-78948600	Weak transcription	Fetal Lung	lung
2	chr3:78937000-78946000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:78937000-78946400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:78938200-78953400	Weak transcription	HepG2	liver
5	chr3:78942600-78946600	Weak transcription	Ovary	ovary
6	chr3:78943200-78946400	Enhancers	Brain Anterior Caudate	brain
7	chr3:78943800-78946400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:78943800-78946600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:78944200-78946000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:78944200-78946200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:78944400-78946000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:78944400-78946000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:78944400-78946000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:78944400-78946200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:78944400-78946200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:78944400-78946400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:78944400-78949000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:78944400-78950200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:78944400-78950200	Weak transcription	Fetal Brain Male	brain
20	chr3:78944800-78946000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:78944800-78946000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:78944800-78946000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:78944800-78946000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:78945000-78946000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:78945000-78950200	Weak transcription	Brain Inferior Temporal Lobe	brain

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