Variant report

Variant	rs6806079
Chromosome Location	chr3:78756474-78756475
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:78741637..78744045-chr3:78754969..78756508,2	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10049014	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10049102	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10428105	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11915494	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11915745	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11917512	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11918759	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11919682	0.81[ASN][1000 genomes]
rs11920344	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11925970	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11927666	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11928868	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12106862	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395784	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17016453	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17016466	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17303276	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17375110	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17375496	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17375739	0.84[ASN][1000 genomes]
rs2031051	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2118068	0.88[ASN][1000 genomes]
rs2271151	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28494803	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3732662	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3732663	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773224	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3773225	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3773226	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3773227	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773231	0.84[ASN][1000 genomes]
rs3773234	0.81[ASN][1000 genomes]
rs3773239	0.81[ASN][1000 genomes]
rs3773240	0.81[ASN][1000 genomes]
rs3773245	0.81[ASN][1000 genomes]
rs3821601	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3821602	0.81[ASN][1000 genomes]
rs3821603	0.81[ASN][1000 genomes]
rs4263256	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56372508	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58561177	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60568341	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60749216	0.93[ASN][1000 genomes]
rs61053911	0.80[ASN][1000 genomes]
rs67137735	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67347336	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67362360	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67498832	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769933	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787349	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6788434	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788511	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73109717	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73109772	0.83[ASN][1000 genomes]
rs73109774	0.81[ASN][1000 genomes]
rs73850750	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610500	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7610686	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7613490	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7616495	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7622194	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7624482	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653782	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs767182	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309810	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9309811	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9309814	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808950	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9818170	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9819398	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9823359	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9829907	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9831098	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9840004	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9840033	0.87[EUR][1000 genomes]
rs9880072	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880316	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882811	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883582	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008156	chr3:78444137-78765884	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	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
3	esv1842222	chr3:78744206-78778901	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	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

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78733800-78778000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:78735200-78765600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr3:78740400-78773800	Weak transcription	Brain Germinal Matrix	brain
4	chr3:78747000-78777400	Weak transcription	Fetal Heart	heart
5	chr3:78749000-78765800	Weak transcription	Ovary	ovary
6	chr3:78749600-78765600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:78752200-78773600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:78752600-78757200	Enhancers	Fetal Stomach	stomach
9	chr3:78752600-78771000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:78753200-78765800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:78753600-78762400	Weak transcription	Brain Anterior Caudate	brain
12	chr3:78753600-78777800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:78754000-78762400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:78754000-78765000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:78754000-78772200	Weak transcription	Brain Substantia Nigra	brain
16	chr3:78755800-78757000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:78755800-78757200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:78756000-78756800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr3:78756000-78757000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:78756000-78757200	Enhancers	Primary T cells from cord blood	blood
21	chr3:78756000-78757200	Enhancers	Fetal Thymus	thymus
22	chr3:78756200-78756600	Enhancers	Muscle Satellite Cultured Cells	--
23	chr3:78756200-78757000	Enhancers	Brain Cingulate Gyrus	brain
24	chr3:78756200-78757000	Enhancers	Colon Smooth Muscle	Colon
25	chr3:78756200-78757200	Enhancers	Brain Hippocampus Middle	brain
26	chr3:78756200-78757200	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr3:78756200-78757400	Enhancers	Fetal Lung	lung
28	chr3:78756200-78765800	Weak transcription	Fetal Muscle Leg	muscle
29	chr3:78756200-78773800	Weak transcription	Fetal Kidney	kidney
30	chr3:78756400-78756600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:78756400-78756800	Enhancers	Osteobl	bone
32	chr3:78756400-78757000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr3:78756400-78757200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:78756400-78758600	Strong transcription	HepG2	liver

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