Variant report

Variant	rs6050939
Chromosome Location	chr20:25838981-25838982
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25604447..25606097-chr20:25837225..25840203,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213742	Chromatin interaction
ENSG00000170191	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs13433200	0.83[ASN][1000 genomes]
rs1977877	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2002942	0.83[ASN][1000 genomes]
rs2380318	0.90[AFR][1000 genomes]
rs4121105	0.83[ASN][1000 genomes]
rs4813595	0.83[ASN][1000 genomes]
rs4815476	0.83[ASN][1000 genomes]
rs4815482	0.83[ASN][1000 genomes]
rs4815489	0.83[ASN][1000 genomes]
rs4815490	0.83[ASN][1000 genomes]
rs4815491	0.83[ASN][1000 genomes]
rs4815494	0.83[ASN][1000 genomes]
rs4815495	0.83[ASN][1000 genomes]
rs4815496	0.83[ASN][1000 genomes]
rs56059532	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59779961	0.83[ASN][1000 genomes]
rs60007971	0.83[ASN][1000 genomes]
rs6037252	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6037270	0.83[ASN][1000 genomes]
rs6037305	0.83[ASN][1000 genomes]
rs6037306	0.83[ASN][1000 genomes]
rs6037307	0.83[ASN][1000 genomes]
rs6037311	0.83[ASN][1000 genomes]
rs6037313	0.83[ASN][1000 genomes]
rs6037314	0.83[ASN][1000 genomes]
rs6050932	0.83[ASN][1000 genomes]
rs6050941	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6050948	0.81[AFR][1000 genomes]
rs6050950	0.84[AFR][1000 genomes]
rs6050958	0.83[EUR][1000 genomes]
rs6051049	0.83[ASN][1000 genomes]
rs6051067	0.83[ASN][1000 genomes]
rs6051072	0.83[ASN][1000 genomes]
rs6051087	0.83[ASN][1000 genomes]
rs6107112	0.83[ASN][1000 genomes]
rs61091356	0.83[ASN][1000 genomes]
rs6115319	0.83[ASN][1000 genomes]
rs6115330	0.83[ASN][1000 genomes]
rs6115340	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6115343	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6115347	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6115350	0.83[ASN][1000 genomes]
rs6115351	0.83[ASN][1000 genomes]
rs6115353	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6115355	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7267539	0.83[ASN][1000 genomes]
rs7268033	0.82[AFR][1000 genomes]
rs7274331	0.83[ASN][1000 genomes]
rs7345455	0.83[ASN][1000 genomes]
rs9653636	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758517	chr20:25701992-26319569	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
2	esv2758790	chr20:25701992-26319569	Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv470545	chr20:25715507-26309255	Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
4	nsv979422	chr20:25732656-25867609	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv10664	chr20:25767042-25849064	Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv585749	chr20:25767347-25856929	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv585752	chr20:25786189-25864851	ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv585753	chr20:25786189-25892571	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv585754	chr20:25786301-25864851	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv585755	chr20:25786301-25871801	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv585756	chr20:25786301-25948094	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv585757	chr20:25786301-25948327	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv585758	chr20:25786984-25951658	Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv585759	chr20:25787096-25948327	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv1059041	chr20:25832105-26007269	Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv1060065	chr20:25832105-26305567	Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
17	nsv9795	chr20:25832369-25851689	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
18	nsv979451	chr20:25836169-25856112	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
19	esv3502991	chr20:25837879-25847973	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
20	esv3502992	chr20:25837879-25847973	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	esv3429566	chr20:25838143-25848095	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25835000-25840200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr20:25837600-25839600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr20:25837800-25840200	Active TSS	Brain Germinal Matrix	brain
4	chr20:25837800-25840200	Active TSS	Fetal Brain Female	brain
5	chr20:25838200-25839200	Active TSS	Brain Cingulate Gyrus	brain
6	chr20:25838200-25839200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr20:25838200-25839800	Active TSS	Brain Angular Gyrus	brain
8	chr20:25838400-25839000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
9	chr20:25838400-25839000	Enhancers	Fetal Brain Male	brain
10	chr20:25838400-25839000	Bivalent Enhancer	Placenta	Placenta
11	chr20:25838400-25839000	Bivalent/Poised TSS	NHEK	skin
12	chr20:25838400-25839200	Active TSS	Brain Substantia Nigra	brain
13	chr20:25838400-25839600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
14	chr20:25838400-25840400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr20:25838400-25842000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
16	chr20:25838400-25842200	ZNF genes & repeats	Dnd41	blood
17	chr20:25838600-25839000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr20:25838600-25839000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
19	chr20:25838600-25839000	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
20	chr20:25838600-25839000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
21	chr20:25838600-25839000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr20:25838600-25839000	Bivalent Enhancer	Colonic Mucosa	Colon
23	chr20:25838600-25839000	ZNF genes & repeats	Pancreas	Pancrea
24	chr20:25838600-25839000	Enhancers	Right Atrium	heart
25	chr20:25838600-25839000	Flanking Bivalent TSS/Enh	HepG2	liver
26	chr20:25838600-25839000	Flanking Active TSS	K562	blood
27	chr20:25838600-25839200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
28	chr20:25838600-25839200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
29	chr20:25838600-25839200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
30	chr20:25838600-25839200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
31	chr20:25838600-25839200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
32	chr20:25838600-25839200	Flanking Active TSS	Esophagus	oesophagus
33	chr20:25838600-25839400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
34	chr20:25838600-25839400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr20:25838600-25839400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
36	chr20:25838600-25839400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
37	chr20:25838600-25839400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr20:25838600-25839400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr20:25838600-25839400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr20:25838600-25839400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
41	chr20:25838600-25839400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr20:25838600-25839400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr20:25838600-25839400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr20:25838600-25839400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
45	chr20:25838600-25839400	Flanking Active TSS	Fetal Heart	heart
46	chr20:25838600-25839400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
47	chr20:25838600-25839400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
48	chr20:25838600-25839400	Bivalent Enhancer	Stomach Mucosa	stomach
49	chr20:25838600-25839400	Bivalent/Poised TSS	NH-A	brain
50	chr20:25838600-25839400	Bivalent Enhancer	NHDF-Ad	bronchial

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