Variant report

Variant	rs9454844
Chromosome Location	chr6:62993749-62993750
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	chr6:62518763..62519292-chr6:62993656..62994388,2	MCF-7	breast:

Extended variants
information (count: 160 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:155)

rs_ID	r²[population]
rs10945156	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10945189	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10945226	0.91[EUR][1000 genomes]
rs1103569	0.90[EUR][1000 genomes]
rs11758619	0.91[EUR][1000 genomes]
rs1204539	0.86[EUR][1000 genomes]
rs1204540	0.86[EUR][1000 genomes]
rs1204543	0.85[EUR][1000 genomes]
rs1204544	0.85[EUR][1000 genomes]
rs12528424	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12660844	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12662273	0.91[EUR][1000 genomes]
rs12663464	0.91[EUR][1000 genomes]
rs16882876	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16883133	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16884023	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16884169	0.91[EUR][1000 genomes]
rs1688991	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs169662	0.86[EUR][1000 genomes]
rs176600	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs176603	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs176604	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs176609	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs176610	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs176612	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs176616	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs176618	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs176619	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs176620	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs176621	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs176622	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1855604	0.81[EUR][1000 genomes]
rs185974	0.86[EUR][1000 genomes]
rs208971	0.81[EUR][1000 genomes]
rs208982	0.81[EUR][1000 genomes]
rs208983	0.83[EUR][1000 genomes]
rs208987	0.86[EUR][1000 genomes]
rs208989	0.86[EUR][1000 genomes]
rs208991	0.86[EUR][1000 genomes]
rs208993	0.86[EUR][1000 genomes]
rs208995	0.86[EUR][1000 genomes]
rs208996	0.85[EUR][1000 genomes]
rs208997	0.85[EUR][1000 genomes]
rs208998	0.85[EUR][1000 genomes]
rs209003	0.85[EUR][1000 genomes]
rs209004	0.85[EUR][1000 genomes]
rs209005	0.86[EUR][1000 genomes]
rs209007	0.86[EUR][1000 genomes]
rs209009	0.87[EUR][1000 genomes]
rs209010	0.87[EUR][1000 genomes]
rs209012	0.84[EUR][1000 genomes]
rs209013	0.90[EUR][1000 genomes]
rs2260966	0.83[EUR][1000 genomes]
rs2345330	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2345331	0.91[EUR][1000 genomes]
rs2492796	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2495266	0.91[EUR][1000 genomes]
rs2495267	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2639412	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2639413	0.91[EUR][1000 genomes]
rs2639414	0.91[EUR][1000 genomes]
rs2639415	0.91[EUR][1000 genomes]
rs2639419	0.83[EUR][1000 genomes]
rs2639446	0.83[EUR][1000 genomes]
rs2639447	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2639448	0.83[EUR][1000 genomes]
rs2639450	0.83[EUR][1000 genomes]
rs2679573	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2814648	0.91[EUR][1000 genomes]
rs2814649	0.91[EUR][1000 genomes]
rs2814650	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2814651	0.91[EUR][1000 genomes]
rs2814652	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2814654	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2814655	0.89[EUR][1000 genomes]
rs2814658	0.83[EUR][1000 genomes]
rs2814659	0.83[EUR][1000 genomes]
rs2814660	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2814678	0.83[EUR][1000 genomes]
rs2814680	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2814681	0.91[EUR][1000 genomes]
rs2842798	0.83[EUR][1000 genomes]
rs2842799	0.83[EUR][1000 genomes]
rs2842802	0.91[EUR][1000 genomes]
rs2842809	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2842810	0.91[EUR][1000 genomes]
rs2842812	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs396074	0.86[EUR][1000 genomes]
rs485617	0.93[EUR][1000 genomes]
rs486719	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs492902	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs494833	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs516904	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517862	0.81[EUR][1000 genomes]
rs524169	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs530011	0.90[EUR][1000 genomes]
rs541351	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs549603	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs550126	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs551082	0.89[EUR][1000 genomes]
rs551124	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs551837	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs555222	0.86[EUR][1000 genomes]
rs567689	0.93[EUR][1000 genomes]
rs567865	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs573454	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs574337	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs577280	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs577542	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs581435	0.81[EUR][1000 genomes]
rs590059	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs591353	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs591366	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs603987	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs606199	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62414796	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62414811	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62416568	0.91[EUR][1000 genomes]
rs62416569	0.91[EUR][1000 genomes]
rs62416570	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62416571	0.83[EUR][1000 genomes]
rs62416572	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs627630	0.81[EUR][1000 genomes]
rs630414	0.81[EUR][1000 genomes]
rs646854	0.81[EUR][1000 genomes]
rs675484	0.81[EUR][1000 genomes]
rs677360	0.81[EUR][1000 genomes]
rs6908177	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6918262	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934952	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73488982	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7742126	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7743214	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7750698	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7770793	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7772645	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs855409	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs855411	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs855412	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs855413	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs855414	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs876854	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9294829	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9294844	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9446114	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9446135	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9446139	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9446154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9454804	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9454831	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9454832	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9454834	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9454845	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9454859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9918343	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017249	chr6:62906813-63317382	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1020677	chr6:62911584-63309663	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv532025	chr6:62944349-63571677	Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv916760	chr6:62944661-63290986	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1034520	chr6:62967960-63057406	Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island 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	chr6:62976400-62994400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:62990400-62994000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:62991800-62996800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:62992600-62994800	Active TSS	Fetal Brain Female	brain
5	chr6:62992600-62997000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:62992800-62994800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:62992800-62997000	Active TSS	Brain Angular Gyrus	brain
8	chr6:62992800-62997000	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr6:62993000-62997000	Active TSS	Fetal Brain Male	brain
10	chr6:62993200-62993800	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr6:62993200-62993800	Active TSS	Brain Anterior Caudate	brain
12	chr6:62993200-62993800	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr6:62993200-62994000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr6:62993200-62996600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:62993400-62993800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr6:62993400-62993800	Active TSS	Brain Cingulate Gyrus	brain
17	chr6:62993400-62993800	Active TSS	Brain Germinal Matrix	brain
18	chr6:62993400-62994200	Enhancers	Primary B cells from peripheral blood	blood
19	chr6:62993400-62994200	Active TSS	Brain Hippocampus Middle	brain
20	chr6:62993400-62996800	Active TSS	Fetal Intestine Small	intestine
21	chr6:62993600-62993800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr6:62993600-62993800	Flanking Active TSS	Fetal Intestine Large	intestine
23	chr6:62993600-62993800	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr6:62993600-62995200	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr6:62993600-62996400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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