Variant report

Variant	rs2028249
Chromosome Location	chr4:68856967-68856968
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	chr4:68854585..68857401-chr4:68944516..68946087,2	MCF-7	breast:

Extended variants
information (count: 179 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10004522	0.81[EUR][1000 genomes]
rs10007054	0.87[ASN][1000 genomes]
rs10018943	0.86[EUR][1000 genomes]
rs1079449	0.86[EUR][1000 genomes]
rs10866201	0.93[ASN][1000 genomes]
rs1109358	1.00[ASN][1000 genomes]
rs1109359	1.00[ASN][1000 genomes]
rs1109360	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11131733	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11131735	0.81[EUR][1000 genomes]
rs11131739	0.81[EUR][1000 genomes]
rs11727567	0.85[EUR][1000 genomes]
rs11731769	0.81[EUR][1000 genomes]
rs11733984	0.87[EUR][1000 genomes]
rs11930532	0.91[ASN][1000 genomes]
rs11931461	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11947862	0.86[EUR][1000 genomes]
rs11947869	0.87[EUR][1000 genomes]
rs12500356	1.00[ASN][1000 genomes]
rs12501405	0.83[EUR][1000 genomes]
rs12501540	0.85[EUR][1000 genomes]
rs12502214	0.81[EUR][1000 genomes]
rs12502757	0.81[EUR][1000 genomes]
rs12502946	0.80[EUR][1000 genomes]
rs12503814	0.83[EUR][1000 genomes]
rs12504120	0.86[EUR][1000 genomes]
rs12504557	0.81[EUR][1000 genomes]
rs12642155	0.89[ASN][1000 genomes]
rs12645384	0.85[EUR][1000 genomes]
rs12648112	0.87[EUR][1000 genomes]
rs12651598	0.81[EUR][1000 genomes]
rs13131396	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13132100	0.87[EUR][1000 genomes]
rs13135438	0.81[EUR][1000 genomes]
rs13147736	0.80[EUR][1000 genomes]
rs1320264	0.81[EUR][1000 genomes]
rs13435884	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1370830	0.84[EUR][1000 genomes]
rs1370840	0.90[ASN][1000 genomes]
rs1438389	0.87[EUR][1000 genomes]
rs1438398	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1438428	0.91[ASN][1000 genomes]
rs1438439	0.87[EUR][1000 genomes]
rs1438440	0.87[EUR][1000 genomes]
rs1438441	0.87[EUR][1000 genomes]
rs1438442	0.87[EUR][1000 genomes]
rs1438443	0.87[EUR][1000 genomes]
rs1438444	0.87[EUR][1000 genomes]
rs1438445	0.87[EUR][1000 genomes]
rs1438447	0.87[EUR][1000 genomes]
rs1530062	0.87[EUR][1000 genomes]
rs1530063	0.87[EUR][1000 genomes]
rs168482	0.88[EUR][1000 genomes]
rs17089005	0.87[EUR][1000 genomes]
rs1837215	0.86[EUR][1000 genomes]
rs1837216	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs184779	0.88[EUR][1000 genomes]
rs184780	0.87[EUR][1000 genomes]
rs1866327	0.86[EUR][1000 genomes]
rs1866328	0.87[EUR][1000 genomes]
rs1866329	0.87[EUR][1000 genomes]
rs189537	0.88[EUR][1000 genomes]
rs1898644	0.86[EUR][1000 genomes]
rs2118625	0.87[EUR][1000 genomes]
rs2164935	0.87[EUR][1000 genomes]
rs2319691	0.88[ASN][1000 genomes]
rs2319718	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28437478	0.90[ASN][1000 genomes]
rs28535832	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34237875	0.81[EUR][1000 genomes]
rs353177	0.86[EUR][1000 genomes]
rs35687408	1.00[ASN][1000 genomes]
rs3819257	0.87[EUR][1000 genomes]
rs4317250	0.81[EUR][1000 genomes]
rs4407557	0.87[EUR][1000 genomes]
rs4538543	0.87[EUR][1000 genomes]
rs4613616	0.87[EUR][1000 genomes]
rs4640716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4860276	0.87[EUR][1000 genomes]
rs4860277	0.87[EUR][1000 genomes]
rs4860278	0.85[EUR][1000 genomes]
rs4860282	0.81[EUR][1000 genomes]
rs4860868	0.90[ASN][1000 genomes]
rs4860875	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4860897	0.87[EUR][1000 genomes]
rs4860908	0.81[EUR][1000 genomes]
rs59098004	0.99[ASN][1000 genomes]
rs59649794	0.82[EUR][1000 genomes]
rs62300800	1.00[ASN][1000 genomes]
rs62300801	1.00[ASN][1000 genomes]
rs6552131	0.90[ASN][1000 genomes]
rs6552132	0.90[ASN][1000 genomes]
rs6552145	0.83[EUR][1000 genomes]
rs6812743	0.85[EUR][1000 genomes]
rs6823814	0.91[ASN][1000 genomes]
rs6827417	0.81[EUR][1000 genomes]
rs6829501	0.90[ASN][1000 genomes]
rs6842578	0.86[EUR][1000 genomes]
rs71604558	0.86[EUR][1000 genomes]
rs7435855	0.87[EUR][1000 genomes]
rs7664796	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7665583	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7674140	0.86[EUR][1000 genomes]
rs7680472	0.90[ASN][1000 genomes]
rs7688501	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688721	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs977728	0.97[ASN][1000 genomes]
rs985274	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:71 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007376	chr4:68693483-69008202	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv879219	chr4:68743032-69028913	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	esv1812791	chr4:68763239-69017739	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	esv1810203	chr4:68763794-68998153	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1812515	chr4:68763794-68998153	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	esv2757939	chr4:68777006-69013364	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv2759257	chr4:68777006-69028913	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	esv1806791	chr4:68781695-69018980	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	esv1808905	chr4:68782651-69020080	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	esv1809262	chr4:68785411-69007019	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	esv1807009	chr4:68786211-68912860	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
12	esv1808371	chr4:68786211-69015416	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	esv1805212	chr4:68786223-69015428	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
14	esv1809085	chr4:68788421-69016619	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
15	esv10683	chr4:68788730-69016101	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
16	nsv10514	chr4:68789515-69015886	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	esv1807372	chr4:68789778-68958980	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
18	esv1805680	chr4:68789778-69001532	Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
19	esv1812567	chr4:68789778-69001532	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
20	esv1805142	chr4:68789778-69017739	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
21	esv1812954	chr4:68789778-69017739	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
22	esv1814820	chr4:68789778-69033099	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
23	esv1805370	chr4:68789778-69043722	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
24	esv1806811	chr4:68790607-69015416	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
25	esv1807563	chr4:68790607-69015416	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
26	esv1806399	chr4:68790619-69009703	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
27	esv1805874	chr4:68790619-69015428	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
28	esv35010	chr4:68790834-69018168	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
29	esv2757060	chr4:68790864-69028913	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
30	esv1813796	chr4:68791144-69008251	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
31	esv1813857	chr4:68791144-69008251	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
32	esv1809432	chr4:68791333-69015820	Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
33	esv1812856	chr4:68791333-69021023	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
34	esv1807026	chr4:68791344-69016756	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
35	esv1804496	chr4:68791400-69013001	Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
36	esv1806212	chr4:68791400-69013001	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
37	esv1807472	chr4:68791400-69013001	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
38	esv1808201	chr4:68791400-69013001	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
39	esv1808500	chr4:68791400-69013001	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
40	esv1811685	chr4:68791400-69013001	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
41	esv1814909	chr4:68791400-69013001	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
42	esv1807658	chr4:68795290-69013001	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
43	esv1807842	chr4:68795815-68877576	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
44	nsv461542	chr4:68797380-68858544	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
45	nsv594502	chr4:68797380-68858544	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
46	nsv461543	chr4:68797380-68877026	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
47	nsv461544	chr4:68797380-68877026	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
48	nsv594503	chr4:68797380-68877026	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
49	nsv461545	chr4:68797380-68877576	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
50	nsv470043	chr4:68797380-68877576	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2028249	GCOM2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:68856600-68857000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr4:68856600-68857000	Flanking Active TSS	Dnd41	blood
3	chr4:68856800-68857000	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr4:68856800-68857000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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