Variant report

Variant	rs60459445
Chromosome Location	chr20:25328112-25328113
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	chr20:25326532..25328200-chr20:25370119..25372568,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100997	Chromatin interaction

Extended variants
information (count: 140 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs12106059	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12106164	1.00[EUR][1000 genomes]
rs12373881	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2500428	1.00[EUR][1000 genomes]
rs28435893	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28439563	1.00[EUR][1000 genomes]
rs28551104	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28733778	1.00[EUR][1000 genomes]
rs35073849	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs417446	1.00[EUR][1000 genomes]
rs56795563	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57237389	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57293656	1.00[EUR][1000 genomes]
rs57522322	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57544952	1.00[AMR][1000 genomes]
rs57579912	1.00[EUR][1000 genomes]
rs58189090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58410604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58593226	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58709664	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58722006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58953621	1.00[AMR][1000 genomes]
rs58957358	1.00[EUR][1000 genomes]
rs59362331	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59431257	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59826126	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59857017	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60479943	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60758360	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60772859	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60831246	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60834749	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60893899	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7264066	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7267807	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7270324	1.00[AMR][1000 genomes]
rs7274585	1.00[AMR][1000 genomes]
rs73331819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73331822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73331824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73331833	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73331834	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73331856	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73331880	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73331881	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73333506	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73333515	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73333541	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73333553	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73333566	1.00[EUR][1000 genomes]
rs73333583	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73333590	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73335304	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73335306	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73335318	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73335323	1.00[AMR][1000 genomes]
rs73335329	1.00[EUR][1000 genomes]
rs73335331	1.00[EUR][1000 genomes]
rs73335348	1.00[EUR][1000 genomes]
rs73335353	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73335363	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73335366	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73335375	1.00[EUR][1000 genomes]
rs73335382	1.00[EUR][1000 genomes]
rs73335383	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73335389	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73335394	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73335398	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73335400	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73335402	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73337199	1.00[EUR][1000 genomes]
rs73337303	1.00[EUR][1000 genomes]
rs73337316	1.00[AMR][1000 genomes]
rs73337317	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73339096	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73339099	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73339100	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341103	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341112	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341114	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341120	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341122	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341124	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341128	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341131	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341135	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341140	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341143	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341155	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341157	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341171	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73343010	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73343043	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73343050	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73343053	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73343058	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73343076	1.00[AMR][1000 genomes]
rs73343090	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73343097	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345003	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345011	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345016	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345021	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345030	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345040	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345068	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345087	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73347016	1.00[AMR][1000 genomes]
rs73347023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73347042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73347058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73347066	1.00[AMR][1000 genomes]
rs8115188	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8117413	1.00[AMR][1000 genomes]
rs8118017	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8120601	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8121557	1.00[EUR][1000 genomes]
rs8123947	1.00[AMR][1000 genomes]
rs9967947	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv482647	chr20:25308912-25481982	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
15	nsv1056997	chr20:25316663-25492339	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
16	nsv1061058	chr20:25327960-25388841	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25292600-25351600	Weak transcription	NHDF-Ad	bronchial
2	chr20:25305000-25331800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr20:25305400-25335000	Weak transcription	Primary B cells from cord blood	blood
4	chr20:25306200-25335800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr20:25309600-25333200	Weak transcription	NHLF	lung
6	chr20:25310200-25332000	Weak transcription	Colon Smooth Muscle	Colon
7	chr20:25310400-25334400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr20:25310600-25334200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr20:25317600-25335600	Weak transcription	Small Intestine	intestine
10	chr20:25319200-25334200	Weak transcription	Right Ventricle	heart
11	chr20:25319200-25348400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr20:25319400-25337000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr20:25319600-25328600	Weak transcription	Fetal Stomach	stomach
14	chr20:25319600-25331400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr20:25319600-25334600	Weak transcription	Fetal Brain Female	brain
16	chr20:25319600-25337000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr20:25319800-25334400	Weak transcription	Fetal Kidney	kidney
18	chr20:25320000-25336800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr20:25321200-25331800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr20:25321200-25334200	Weak transcription	Ovary	ovary
21	chr20:25321400-25331800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr20:25322200-25334200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr20:25322400-25336600	Weak transcription	Fetal Heart	heart
24	chr20:25322800-25331000	Weak transcription	Fetal Intestine Small	intestine
25	chr20:25323400-25333400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr20:25323600-25333000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr20:25323600-25333200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr20:25324200-25331000	Weak transcription	Pancreas	Pancrea
29	chr20:25324200-25333400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr20:25324200-25337200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr20:25324400-25334200	Weak transcription	Left Ventricle	heart
32	chr20:25325400-25331400	Weak transcription	Brain Angular Gyrus	brain
33	chr20:25325400-25334200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr20:25325400-25334200	Weak transcription	GM12878-XiMat	blood
35	chr20:25325400-25336600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr20:25325600-25331400	Weak transcription	Brain Hippocampus Middle	brain
37	chr20:25325600-25333600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr20:25325600-25334200	Weak transcription	A549	lung
39	chr20:25325600-25336600	Weak transcription	Dnd41	blood
40	chr20:25327000-25328800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr20:25327400-25361400	Weak transcription	Primary T cells from cord blood	blood
42	chr20:25327800-25335600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr20:25328000-25337000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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