Variant report

Variant	rs6050486
Chromosome Location	chr20:25230841-25230842
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25228557..25231308-chr20:25476839..25479017,2	MCF-7	breast:
2	chr20:25189131..25190922-chr20:25228814..25231748,2	MCF-7	breast:
3	chr20:25174902..25179249-chr20:25225017..25231959,9	MCF-7	breast:
4	chr20:25202506..25206898-chr20:25226343..25231297,7	MCF-7	breast:
5	chr12:53339776..53342666-chr20:25227973..25230849,2	MCF-7	breast:
6	chr20:25119092..25121344-chr20:25229044..25231163,2	MCF-7	breast:
7	chr20:25174010..25179528-chr20:25225802..25231331,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197586	Chromatin interaction
ENSG00000101004	Chromatin interaction
ENSG00000111057	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs11905042	0.83[YRI][hapmap]
rs11907515	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2067793	0.81[ASW][hapmap];1.00[EUR][1000 genomes]
rs2145125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2180596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2180597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2228978	1.00[EUR][1000 genomes]
rs2387734	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28496800	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28770021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28881233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34299454	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41282340	1.00[EUR][1000 genomes]
rs41304802	1.00[EUR][1000 genomes]
rs41308633	1.00[EUR][1000 genomes]
rs58412968	0.83[EUR][1000 genomes]
rs58953621	0.83[EUR][1000 genomes]
rs59082275	0.83[EUR][1000 genomes]
rs6037061	1.00[CEU][hapmap];0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs6037064	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6037068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6037070	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6037071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6037073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6037075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050449	1.00[EUR][1000 genomes]
rs6050451	1.00[EUR][1000 genomes]
rs6050457	1.00[EUR][1000 genomes]
rs6050458	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6050459	1.00[ASW][hapmap];0.89[YRI][hapmap]
rs6050461	1.00[EUR][1000 genomes]
rs6050462	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6050465	1.00[EUR][1000 genomes]
rs6050471	1.00[CEU][hapmap]
rs6050473	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050474	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050476	1.00[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050478	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050485	0.83[AFR][1000 genomes]
rs6050487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050495	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6050502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050505	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6050507	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050508	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050509	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050510	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050511	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050512	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7263527	1.00[EUR][1000 genomes]
rs7266033	1.00[CEU][hapmap]
rs7269045	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7273544	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7274919	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73343076	0.83[EUR][1000 genomes]
rs73347016	0.83[EUR][1000 genomes]
rs73347066	0.83[EUR][1000 genomes]
rs7344105	1.00[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs736358	1.00[EUR][1000 genomes]
rs8116564	1.00[EUR][1000 genomes]
rs8118763	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8120268	1.00[EUR][1000 genomes]
rs8123947	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs8125980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8126469	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv1066667	chr20:25133066-25238976	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	nsv544222	chr20:25133066-25238976	Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	nsv828708	chr20:25223895-25231601	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25227600-25231200	Active TSS	Sigmoid Colon	Sigmoid Colon
2	chr20:25227800-25231000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr20:25227800-25231200	Active TSS	Left Ventricle	heart
4	chr20:25227800-25231600	Active TSS	Right Atrium	heart
5	chr20:25228200-25232400	Active TSS	Right Ventricle	heart
6	chr20:25228400-25231000	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr20:25228400-25231000	Active TSS	GM12878-XiMat	blood
8	chr20:25228600-25231000	Active TSS	NHLF	lung
9	chr20:25229600-25231200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr20:25229600-25231400	Enhancers	Spleen	Spleen
11	chr20:25229800-25231000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr20:25229800-25231200	Enhancers	Fetal Intestine Large	intestine
13	chr20:25229800-25231800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr20:25229800-25232000	Enhancers	Primary T cells fromperipheralblood	blood
15	chr20:25229800-25233000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr20:25229800-25233400	Weak transcription	Placenta	Placenta
17	chr20:25229800-25235400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr20:25229800-25250000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr20:25230000-25231000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr20:25230000-25231000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr20:25230000-25231400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
22	chr20:25230000-25231400	Enhancers	Fetal Muscle Leg	muscle
23	chr20:25230000-25231400	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr20:25230000-25231400	Transcr. at gene 5' and 3'	A549	lung
25	chr20:25230000-25231400	Flanking Active TSS	NH-A	brain
26	chr20:25230000-25231800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr20:25230000-25232000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr20:25230200-25231000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr20:25230200-25231200	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr20:25230200-25231200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr20:25230200-25231200	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr20:25230200-25231200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr20:25230200-25231200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr20:25230200-25231400	Enhancers	H1 Cell Line	embryonic stem cell
35	chr20:25230200-25231400	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr20:25230200-25231400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr20:25230200-25231400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr20:25230200-25231400	Enhancers	Duodenum Mucosa	Duodenum
39	chr20:25230200-25231400	Enhancers	Small Intestine	intestine
40	chr20:25230200-25231400	Enhancers	K562	blood
41	chr20:25230200-25231600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr20:25230200-25231800	Weak transcription	Thymus	Thymus
43	chr20:25230200-25232000	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr20:25230200-25232600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr20:25230200-25232800	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr20:25230200-25233200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr20:25230200-25233200	Enhancers	Fetal Brain Male	brain
48	chr20:25230200-25234000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr20:25230200-25235400	Weak transcription	Primary B cells from peripheral blood	blood
50	chr20:25230200-25235800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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