Variant report

Variant	rs2500411
Chromosome Location	chr20:25254840-25254841
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25252960..25255983-chr20:25260897..25264213,3	MCF-7	breast:
2	chr20:24973494..24975181-chr20:25253726..25255240,2	MCF-7	breast:
3	chr20:25253122..25255377-chr20:25264937..25266840,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101474	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs2039400	1.00[AMR][1000 genomes]
rs2258671	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2258672	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2474768	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2474770	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2474772	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2474775	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2474776	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482907	1.00[AMR][1000 genomes]
rs2482909	1.00[AMR][1000 genomes]
rs2482916	1.00[AMR][1000 genomes]
rs2482917	1.00[AMR][1000 genomes]
rs2482920	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482922	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482925	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482929	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482939	1.00[AMR][1000 genomes]
rs2482942	1.00[AMR][1000 genomes]
rs2482945	1.00[AMR][1000 genomes]
rs2500394	1.00[AMR][1000 genomes]
rs2500396	1.00[AMR][1000 genomes]
rs2500402	1.00[AMR][1000 genomes]
rs2500407	1.00[AMR][1000 genomes]
rs2500409	1.00[AMR][1000 genomes]
rs2500412	1.00[AMR][1000 genomes]
rs2500414	1.00[AMR][1000 genomes]
rs2500419	1.00[AMR][1000 genomes]
rs2500420	1.00[AMR][1000 genomes]
rs2500429	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500431	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500434	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500435	0.80[AFR][1000 genomes]
rs2500437	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500438	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500440	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500444	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500445	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500447	1.00[AMR][1000 genomes]
rs2983490	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2990515	1.00[AMR][1000 genomes]
rs3002699	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3002700	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3002703	1.00[AMR][1000 genomes]
rs368636	1.00[AMR][1000 genomes]
rs380021	1.00[AMR][1000 genomes]
rs426143	1.00[AMR][1000 genomes]
rs448866	1.00[AMR][1000 genomes]
rs6037066	0.81[AFR][1000 genomes]
rs6037089	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6037119	1.00[AMR][1000 genomes]
rs6050450	0.80[AFR][1000 genomes]
rs6050480	0.85[AFR][1000 genomes]
rs6050591	1.00[AMR][1000 genomes]
rs6050613	1.00[AMR][1000 genomes]
rs6050618	1.00[AMR][1000 genomes]
rs6050627	1.00[AMR][1000 genomes]
rs73904034	0.85[AFR][1000 genomes]
rs73904036	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73904038	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73904039	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
11	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
12	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
14	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
15	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
16	nsv833948	chr20:25231726-25410540	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
17	esv1798601	chr20:25250122-25305949	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25230400-25291600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr20:25235600-25291200	Weak transcription	Fetal Kidney	kidney
3	chr20:25237600-25262800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr20:25241000-25258200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr20:25241800-25273200	Weak transcription	Stomach Mucosa	stomach
6	chr20:25242800-25258000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr20:25243000-25269600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr20:25246800-25259400	Strong transcription	HMEC	breast
9	chr20:25247400-25258000	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr20:25247600-25277400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr20:25249000-25255400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr20:25249000-25280200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr20:25249200-25256400	Strong transcription	HSMM	muscle
14	chr20:25249200-25274800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr20:25249200-25275000	Strong transcription	A549	lung
16	chr20:25249200-25285800	Strong transcription	Dnd41	blood
17	chr20:25249400-25256000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr20:25249400-25262000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr20:25249400-25274600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr20:25249400-25274800	Strong transcription	Osteobl	bone
21	chr20:25249400-25276200	Strong transcription	Fetal Intestine Large	intestine
22	chr20:25249600-25255400	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr20:25249600-25255800	Genic enhancers	Left Ventricle	heart
24	chr20:25249600-25258400	Strong transcription	HepG2	liver
25	chr20:25249600-25261400	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr20:25249600-25261800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr20:25249600-25267000	Strong transcription	NH-A	brain
28	chr20:25249600-25273400	Strong transcription	NHEK	skin
29	chr20:25249600-25274400	Strong transcription	Lung	lung
30	chr20:25249600-25274600	Strong transcription	Primary T cells from cord blood	blood
31	chr20:25249600-25274600	Strong transcription	Duodenum Mucosa	Duodenum
32	chr20:25249600-25274800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr20:25249600-25275000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr20:25249600-25275000	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr20:25249600-25275000	Strong transcription	NHLF	lung
36	chr20:25249600-25275200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr20:25249600-25279000	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr20:25249600-25279400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr20:25249600-25284800	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr20:25249600-25285200	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr20:25249800-25255000	Strong transcription	Fetal Lung	lung
42	chr20:25249800-25255200	Strong transcription	NHDF-Ad	bronchial
43	chr20:25249800-25256400	Strong transcription	Ovary	ovary
44	chr20:25249800-25256800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr20:25249800-25258800	Strong transcription	Colonic Mucosa	Colon
46	chr20:25249800-25260600	Strong transcription	Spleen	Spleen
47	chr20:25249800-25261000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr20:25249800-25261800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr20:25249800-25262000	Strong transcription	Fetal Muscle Leg	muscle
50	chr20:25249800-25264800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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