Variant report

Variant	rs41282340
Chromosome Location	chr20:25277231-25277232
allele	C/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:25274484..25277309-chr20:25281088..25284844,3	MCF-7	breast:
2	chr20:25277010..25279912-chr20:25462998..25464763,2	K562	blood:
3	chr20:25226304..25227809-chr20:25275139..25278038,2	MCF-7	breast:
4	chr20:25275341..25277928-chr20:25277933..25279564,2	MCF-7	breast:
5	chr20:25159530..25160087-chr20:25276913..25277799,2	MCF-7	breast:
6	chr20:25274719..25277448-chr20:25283422..25285264,2	K562	blood:
7	chr20:25275257..25278068-chr20:25368831..25372041,3	MCF-7	breast:
8	chr20:25236219..25236723-chr20:25276860..25277785,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000100997	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11907515	1.00[EUR][1000 genomes]
rs2067793	1.00[EUR][1000 genomes]
rs2145125	1.00[EUR][1000 genomes]
rs2180596	1.00[EUR][1000 genomes]
rs2180597	1.00[EUR][1000 genomes]
rs2228978	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2387734	1.00[EUR][1000 genomes]
rs28496800	1.00[EUR][1000 genomes]
rs28770021	1.00[EUR][1000 genomes]
rs28881233	1.00[EUR][1000 genomes]
rs34299454	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[EUR][1000 genomes]
rs6037064	1.00[EUR][1000 genomes]
rs6037068	1.00[EUR][1000 genomes]
rs6037070	1.00[EUR][1000 genomes]
rs6037071	1.00[EUR][1000 genomes]
rs6037073	1.00[EUR][1000 genomes]
rs6037075	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[EUR][1000 genomes]
rs6050461	1.00[EUR][1000 genomes]
rs6050462	1.00[EUR][1000 genomes]
rs6050465	1.00[EUR][1000 genomes]
rs6050473	1.00[EUR][1000 genomes]
rs6050474	1.00[EUR][1000 genomes]
rs6050476	1.00[EUR][1000 genomes]
rs6050478	1.00[EUR][1000 genomes]
rs6050486	1.00[EUR][1000 genomes]
rs6050487	1.00[EUR][1000 genomes]
rs6050488	1.00[EUR][1000 genomes]
rs6050490	1.00[EUR][1000 genomes]
rs6050492	1.00[EUR][1000 genomes]
rs6050493	1.00[EUR][1000 genomes]
rs6050494	1.00[EUR][1000 genomes]
rs6050502	1.00[EUR][1000 genomes]
rs6050503	1.00[EUR][1000 genomes]
rs6050504	1.00[EUR][1000 genomes]
rs6050507	1.00[EUR][1000 genomes]
rs6050508	1.00[EUR][1000 genomes]
rs6050509	1.00[EUR][1000 genomes]
rs6050510	1.00[EUR][1000 genomes]
rs6050511	1.00[EUR][1000 genomes]
rs7263527	1.00[EUR][1000 genomes]
rs7269045	1.00[EUR][1000 genomes]
rs7273544	1.00[EUR][1000 genomes]
rs7274919	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[EUR][1000 genomes]
rs736358	1.00[EUR][1000 genomes]
rs8116564	1.00[EUR][1000 genomes]
rs8118763	1.00[EUR][1000 genomes]
rs8120268	1.00[EUR][1000 genomes]
rs8123947	0.83[EUR][1000 genomes]
rs8125980	1.00[EUR][1000 genomes]

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	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
18	nsv912827	chr20:25271326-25288632	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 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	chr20:25235600-25291200	Weak transcription	Fetal Kidney	kidney
3	chr20:25247600-25277400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr20:25249000-25280200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr20:25249200-25285800	Strong transcription	Dnd41	blood
6	chr20:25249600-25279000	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr20:25249600-25279400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr20:25249600-25284800	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr20:25249600-25285200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr20:25249800-25284400	Strong transcription	Brain Germinal Matrix	brain
11	chr20:25250800-25285000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr20:25254400-25287800	Weak transcription	K562	blood
13	chr20:25255600-25279200	Strong transcription	Fetal Brain Female	brain
14	chr20:25255800-25290000	Weak transcription	Small Intestine	intestine
15	chr20:25256000-25299400	Weak transcription	Fetal Brain Male	brain
16	chr20:25259000-25290800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr20:25261600-25291000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr20:25266600-25291200	Weak transcription	Primary B cells from cord blood	blood
19	chr20:25267000-25291200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr20:25267600-25279200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr20:25269200-25281600	Weak transcription	Liver	Liver
22	chr20:25270400-25278800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr20:25271400-25279600	Genic enhancers	HMEC	breast
24	chr20:25271400-25290600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr20:25271600-25291200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr20:25272400-25277600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr20:25272800-25282400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr20:25273400-25277400	Genic enhancers	NHEK	skin
29	chr20:25273400-25277600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr20:25273400-25277800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr20:25273400-25278000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr20:25273400-25287200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr20:25274000-25278600	Genic enhancers	Stomach Smooth Muscle	stomach
34	chr20:25274200-25277400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr20:25274200-25277400	Genic enhancers	Colon Smooth Muscle	Colon
36	chr20:25274400-25278400	Genic enhancers	Fetal Muscle Leg	muscle
37	chr20:25274400-25278400	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr20:25274600-25277800	Genic enhancers	Fetal Muscle Trunk	muscle
39	chr20:25274600-25277800	Genic enhancers	Gastric	stomach
40	chr20:25274600-25277800	Enhancers	Psoas Muscle	Psoas
41	chr20:25274600-25278400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr20:25274600-25278800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr20:25274800-25278800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr20:25274800-25278800	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr20:25274800-25280800	Weak transcription	Aorta	Aorta
46	chr20:25275000-25277400	Genic enhancers	Muscle Satellite Cultured Cells	--
47	chr20:25275000-25277400	Genic enhancers	HepG2	liver
48	chr20:25275000-25277800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr20:25275000-25277800	Genic enhancers	NHLF	lung
50	chr20:25275000-25278600	Genic enhancers	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links