Variant report

Variant	rs2474772
Chromosome Location	chr20:25250163-25250164
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	chr20:25248981..25251939-chr20:25255782..25258389,2	MCF-7	breast:
2	chr20:25248500..25251433-chr20:25251718..25254051,3	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs2039400	1.00[ASW][hapmap];0.85[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs2258671	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2258672	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2474768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2474770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2474775	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2474776	0.80[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	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482922	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482925	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482929	1.00[AMR][1000 genomes]
rs2482939	1.00[ASW][hapmap];0.85[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.91[YRI][hapmap];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	0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs2500409	1.00[AMR][1000 genomes]
rs2500411	0.87[AFR][1000 genomes];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]
rs2500421	1.00[MEX][hapmap]
rs2500429	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500431	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500434	0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs2500437	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500438	0.91[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500440	1.00[AMR][1000 genomes]
rs2500444	1.00[AMR][1000 genomes]
rs2500445	1.00[AMR][1000 genomes]
rs2500447	1.00[AMR][1000 genomes]
rs2983490	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2990515	1.00[AMR][1000 genomes]
rs3002699	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3002700	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3002703	1.00[AMR][1000 genomes]
rs448866	1.00[AMR][1000 genomes]
rs6037066	0.85[AFR][1000 genomes]
rs6037089	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6037118	1.00[MEX][hapmap]
rs6037119	0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs6050450	1.00[GIH][hapmap]
rs6050480	0.89[AFR][1000 genomes]
rs6050591	1.00[AMR][1000 genomes]
rs6050613	1.00[AMR][1000 genomes]
rs6050618	0.80[YRI][hapmap];1.00[AMR][1000 genomes]
rs6050627	1.00[ASW][hapmap];0.85[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs73904034	0.89[AFR][1000 genomes]
rs73904036	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73904038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73904039	1.00[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:123 , 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	chr20:25231200-25251800	Weak transcription	Hela-S3	cervix
3	chr20:25231200-25252200	Weak transcription	HUVEC	blood vessel
4	chr20:25233200-25252200	Weak transcription	Fetal Brain Male	brain
5	chr20:25235600-25291200	Weak transcription	Fetal Kidney	kidney
6	chr20:25236200-25251600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr20:25236600-25253800	Weak transcription	Psoas Muscle	Psoas
8	chr20:25237600-25262800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr20:25240800-25251400	Weak transcription	Thymus	Thymus
10	chr20:25241000-25258200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr20:25241400-25251600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr20:25241400-25252600	Weak transcription	Primary B cells from cord blood	blood
13	chr20:25241600-25250200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr20:25241600-25251800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr20:25241800-25273200	Weak transcription	Stomach Mucosa	stomach
16	chr20:25242000-25250200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr20:25242000-25251600	Weak transcription	Fetal Thymus	thymus
18	chr20:25242800-25251800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr20:25242800-25258000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr20:25243000-25269600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr20:25246400-25253000	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr20:25246800-25259400	Strong transcription	HMEC	breast
23	chr20:25247000-25250400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr20:25247400-25258000	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr20:25247600-25277400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr20:25249000-25255400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr20:25249000-25280200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr20:25249200-25251000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr20:25249200-25252200	Strong transcription	Brain Substantia Nigra	brain
30	chr20:25249200-25256400	Strong transcription	HSMM	muscle
31	chr20:25249200-25274800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr20:25249200-25275000	Strong transcription	A549	lung
33	chr20:25249200-25285800	Strong transcription	Dnd41	blood
34	chr20:25249400-25256000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr20:25249400-25262000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr20:25249400-25274600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr20:25249400-25274800	Strong transcription	Osteobl	bone
38	chr20:25249400-25276200	Strong transcription	Fetal Intestine Large	intestine
39	chr20:25249600-25250800	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr20:25249600-25251000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr20:25249600-25251600	Strong transcription	Stomach Smooth Muscle	stomach
42	chr20:25249600-25252400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr20:25249600-25252600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr20:25249600-25253000	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr20:25249600-25253400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr20:25249600-25254200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr20:25249600-25255400	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr20:25249600-25255800	Genic enhancers	Left Ventricle	heart
49	chr20:25249600-25258400	Strong transcription	HepG2	liver
50	chr20:25249600-25261400	Strong transcription	Primary T cells fromperipheralblood	blood

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