Variant report

Variant	rs6797304
Chromosome Location	chr3:178831715-178831716
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:178830287..178832658-chr3:179039963..179041863,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121864	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1059691	0.90[ASN][1000 genomes]
rs10936992	0.86[ASN][1000 genomes]
rs11706842	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708869	1.00[ASN][1000 genomes]
rs11918324	0.97[ASN][1000 genomes]
rs11918587	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919383	0.90[ASN][1000 genomes]
rs11920864	0.80[EUR][1000 genomes]
rs11922631	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11924545	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11924547	1.00[ASN][1000 genomes]
rs11924600	0.89[ASN][1000 genomes]
rs11925655	1.00[ASN][1000 genomes]
rs12488074	0.88[ASN][1000 genomes]
rs1568205	0.88[ASN][1000 genomes]
rs17849071	0.97[ASN][1000 genomes]
rs1850504	1.00[ASN][1000 genomes]
rs1970901	0.88[ASN][1000 genomes]
rs1976765	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2865082	0.97[ASN][1000 genomes]
rs3729674	0.88[ASN][1000 genomes]
rs3729676	0.88[ASN][1000 genomes]
rs3729682	0.97[ASN][1000 genomes]
rs3729694	0.97[ASN][1000 genomes]
rs3975513	0.88[ASN][1000 genomes]
rs3976507	1.00[ASN][1000 genomes]
rs4080957	0.90[ASN][1000 genomes]
rs4855093	1.00[ASN][1000 genomes]
rs55685804	0.97[ASN][1000 genomes]
rs55933053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55961756	0.97[ASN][1000 genomes]
rs56023503	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56095736	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56143971	0.97[ASN][1000 genomes]
rs56372555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56378415	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56748382	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs57299654	0.82[ASN][1000 genomes]
rs59340081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59408989	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59922883	1.00[ASN][1000 genomes]
rs61796482	0.97[ASN][1000 genomes]
rs61796483	0.90[ASN][1000 genomes]
rs62408837	0.82[ASN][1000 genomes]
rs6443619	0.90[ASN][1000 genomes]
rs6443624	0.90[ASN][1000 genomes]
rs6443625	0.88[ASN][1000 genomes]
rs6443626	1.00[ASN][1000 genomes]
rs6443627	1.00[ASN][1000 genomes]
rs6443628	0.90[ASN][1000 genomes]
rs6443629	0.93[ASN][1000 genomes]
rs67562832	0.95[ASN][1000 genomes]
rs67609137	1.00[ASN][1000 genomes]
rs6765953	0.97[ASN][1000 genomes]
rs6767284	1.00[ASN][1000 genomes]
rs6769154	0.90[ASN][1000 genomes]
rs6769162	0.90[ASN][1000 genomes]
rs6769508	1.00[ASN][1000 genomes]
rs6770267	1.00[ASN][1000 genomes]
rs6771313	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6774158	0.97[ASN][1000 genomes]
rs6777203	0.97[ASN][1000 genomes]
rs6782557	0.90[ASN][1000 genomes]
rs6786114	0.90[ASN][1000 genomes]
rs6791153	0.97[ASN][1000 genomes]
rs67920954	0.97[ASN][1000 genomes]
rs6792189	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794252	0.86[ASN][1000 genomes]
rs6798817	0.90[ASN][1000 genomes]
rs6799756	1.00[ASN][1000 genomes]
rs6803076	0.88[ASN][1000 genomes]
rs6803219	0.88[ASN][1000 genomes]
rs6806555	1.00[ASN][1000 genomes]
rs6806917	0.90[ASN][1000 genomes]
rs6810246	1.00[ASN][1000 genomes]
rs73051974	1.00[ASN][1000 genomes]
rs73187218	0.80[EUR][1000 genomes]
rs73187223	0.83[EUR][1000 genomes]
rs73187225	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs73187264	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73187276	0.97[ASN][1000 genomes]
rs7372645	0.90[ASN][1000 genomes]
rs7612533	1.00[ASN][1000 genomes]
rs7614305	0.88[ASN][1000 genomes]
rs7614418	0.97[ASN][1000 genomes]
rs7615076	0.90[ASN][1000 genomes]
rs7621329	0.90[ASN][1000 genomes]
rs7621436	0.90[ASN][1000 genomes]
rs7623154	0.97[ASN][1000 genomes]
rs7624090	0.97[ASN][1000 genomes]
rs7627273	1.00[ASN][1000 genomes]
rs7628855	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636454	0.97[ASN][1000 genomes]
rs7638323	0.97[ASN][1000 genomes]
rs7638525	0.83[EUR][1000 genomes]
rs7638649	1.00[ASN][1000 genomes]
rs7641889	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641983	0.90[ASN][1000 genomes]
rs7645550	0.82[ASN][1000 genomes]
rs7646409	0.88[ASN][1000 genomes]
rs7648857	1.00[ASN][1000 genomes]
rs7650809	0.83[ASN][1000 genomes]
rs7651265	1.00[ASN][1000 genomes]
rs7651371	0.83[EUR][1000 genomes]
rs938752	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9631497	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9813190	0.90[ASN][1000 genomes]
rs9819762	0.97[ASN][1000 genomes]
rs9829903	0.90[ASN][1000 genomes]
rs9831234	0.90[ASN][1000 genomes]
rs9833438	0.90[ASN][1000 genomes]
rs9838411	1.00[ASN][1000 genomes]
rs9839519	1.00[ASN][1000 genomes]
rs9841051	0.88[ASN][1000 genomes]
rs9844270	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9844482	0.90[ASN][1000 genomes]
rs9850621	1.00[ASN][1000 genomes]
rs9862294	0.95[ASN][1000 genomes]
rs9866361	0.88[ASN][1000 genomes]
rs9877812	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881887	0.95[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	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	52 gene(s)	inside rSNPs	diseases
3	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription 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	22 gene(s)	inside rSNPs	diseases
4	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv1792927	chr3:178734558-178877169	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	esv1841799	chr3:178739594-178884337	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv878037	chr3:178825910-178871906	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178826600-178833000	Weak transcription	Osteobl	bone
2	chr3:178827200-178832800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:178827200-178832800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:178829800-178833000	Weak transcription	HUVEC	blood vessel
5	chr3:178830800-178833800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:178831600-178832200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:178831600-178832400	Enhancers	Muscle Satellite Cultured Cells	--
8	chr3:178831600-178832400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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