Variant report

Variant	rs28435893
Chromosome Location	chr20:25217124-25217125
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:25186090..25188287-chr20:25215991..25218465,2	MCF-7	breast:
2	chr20:25183250..25185573-chr20:25216058..25218999,2	K562	blood:
3	chr20:25202630..25205811-chr20:25216329..25219986,4	MCF-7	breast:
4	chr20:25204290..25209975-chr20:25213026..25218082,9	K562	blood:
5	chr20:25200803..25202530-chr20:25217099..25219060,2	MCF-7	breast:
6	chr20:25182714..25185445-chr20:25216908..25218844,2	MCF-7	breast:
7	chr20:25212487..25223003-chr20:25225155..25231821,24	MCF-7	breast:
8	chr20:25210927..25216331-chr20:25216727..25222043,13	MCF-7	breast:
9	chr20:25204290..25212190-chr20:25213333..25218082,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000197586	Chromatin interaction
ENSG00000268302	Chromatin interaction
ENSG00000100994	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs11907003	1.00[EUR][1000 genomes]
rs11908037	1.00[EUR][1000 genomes]
rs12106059	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12106164	1.00[EUR][1000 genomes]
rs12373881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2500428	1.00[EUR][1000 genomes]
rs28439563	1.00[EUR][1000 genomes]
rs28551104	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35022349	1.00[EUR][1000 genomes]
rs35073849	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56273742	1.00[EUR][1000 genomes]
rs57218388	1.00[EUR][1000 genomes]
rs57293656	1.00[EUR][1000 genomes]
rs58189090	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58410604	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58593226	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58709664	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58722006	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58953621	1.00[AMR][1000 genomes]
rs58957358	1.00[EUR][1000 genomes]
rs59431257	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59857017	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60459445	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60479943	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050367	1.00[EUR][1000 genomes]
rs60893899	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6106987	1.00[EUR][1000 genomes]
rs7270236	1.00[EUR][1000 genomes]
rs7270324	1.00[AMR][1000 genomes]
rs7274585	1.00[AMR][1000 genomes]
rs73331819	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73331822	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73331824	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	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]
rs73333142	1.00[EUR][1000 genomes]
rs73333167	1.00[EUR][1000 genomes]
rs73333174	1.00[EUR][1000 genomes]
rs73333187	1.00[EUR][1000 genomes]
rs73333506	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73333515	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73337199	1.00[EUR][1000 genomes]
rs73339096	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73339099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73339100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341120	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341122	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341124	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341128	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341131	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341135	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341140	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341143	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341155	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341157	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341171	0.85[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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73343050	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73343053	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73343058	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73343076	1.00[AMR][1000 genomes]
rs73343090	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73343097	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345003	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345011	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345016	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345021	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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345069	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345071	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345073	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345082	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345087	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345088	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73347016	1.00[AMR][1000 genomes]
rs73347023	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73347042	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73347058	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73347066	1.00[AMR][1000 genomes]
rs73348712	1.00[EUR][1000 genomes]
rs73906055	1.00[EUR][1000 genomes]
rs73906057	1.00[EUR][1000 genomes]
rs73906063	1.00[EUR][1000 genomes]
rs73906065	1.00[EUR][1000 genomes]
rs73906067	1.00[EUR][1000 genomes]
rs73906068	1.00[EUR][1000 genomes]
rs73906070	1.00[EUR][1000 genomes]
rs73906071	1.00[EUR][1000 genomes]
rs73906072	1.00[EUR][1000 genomes]
rs8114108	1.00[EUR][1000 genomes]
rs8115188	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8117413	1.00[AMR][1000 genomes]
rs8118017	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8119273	1.00[EUR][1000 genomes]
rs8120601	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8121557	1.00[EUR][1000 genomes]
rs8123929	1.00[EUR][1000 genomes]
rs8123947	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	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

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25204200-25222800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr20:25204400-25218200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr20:25206800-25218200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr20:25207800-25218200	Weak transcription	Spleen	Spleen
5	chr20:25207800-25218200	Weak transcription	Dnd41	blood
6	chr20:25208600-25218200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr20:25209200-25218200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr20:25210800-25218200	Weak transcription	Lung	lung
9	chr20:25210800-25218400	Weak transcription	Brain Hippocampus Middle	brain
10	chr20:25211200-25217600	Weak transcription	Aorta	Aorta
11	chr20:25211200-25218600	Weak transcription	Brain Anterior Caudate	brain
12	chr20:25212000-25218400	Weak transcription	Colon Smooth Muscle	Colon
13	chr20:25213200-25221800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr20:25213400-25222200	Enhancers	HMEC	breast
15	chr20:25213600-25222200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr20:25213800-25220200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr20:25214200-25218200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr20:25214200-25218800	Enhancers	Muscle Satellite Cultured Cells	--
19	chr20:25214200-25220800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr20:25214400-25217400	Weak transcription	Pancreas	Pancrea
21	chr20:25214400-25218000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr20:25214400-25218000	Weak transcription	Psoas Muscle	Psoas
23	chr20:25214400-25218000	Weak transcription	Right Ventricle	heart
24	chr20:25214400-25218000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr20:25214400-25218200	Weak transcription	Left Ventricle	heart
26	chr20:25214400-25218200	Weak transcription	Ovary	ovary
27	chr20:25214400-25218400	Enhancers	NHEK	skin
28	chr20:25214400-25219400	Enhancers	Stomach Mucosa	stomach
29	chr20:25214400-25223000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr20:25214600-25217200	Weak transcription	NH-A	brain
31	chr20:25214600-25218200	Weak transcription	HUVEC	blood vessel
32	chr20:25215200-25218000	Enhancers	Hela-S3	cervix
33	chr20:25215200-25218800	Enhancers	Osteobl	bone
34	chr20:25215200-25221800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr20:25215400-25217400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr20:25215400-25219600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr20:25215400-25223200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr20:25215600-25217200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr20:25215600-25217600	Weak transcription	Right Atrium	heart
40	chr20:25215600-25218400	Weak transcription	Brain Angular Gyrus	brain
41	chr20:25215600-25221600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr20:25215800-25217200	Weak transcription	NHDF-Ad	bronchial
43	chr20:25215800-25217400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr20:25215800-25217400	Weak transcription	HSMM	muscle
45	chr20:25215800-25217400	Weak transcription	K562	blood
46	chr20:25215800-25218000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr20:25215800-25218200	Enhancers	A549	lung
48	chr20:25215800-25218600	Weak transcription	Fetal Heart	heart
49	chr20:25215800-25219600	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr20:25215800-25221600	Weak transcription	Fetal Kidney	kidney

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