Variant report

Variant	rs73339040
Chromosome Location	chr20:25187335-25187336
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25185473..25187365-chr20:25194994..25197584,2	K562	blood:
2	chr20:25184070..25187780-chr20:25226267..25231211,5	MCF-7	breast:
3	chr20:25185632..25187734-chr20:25204064..25206266,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100994	Chromatin interaction
ENSG00000202414	Chromatin interaction
ENSG00000197586	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11907597	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41282324	1.00[EUR][1000 genomes]
rs59364512	1.00[EUR][1000 genomes]
rs6050340	1.00[EUR][1000 genomes]
rs6050437	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73333159	1.00[EUR][1000 genomes]
rs73333163	1.00[EUR][1000 genomes]
rs73333170	1.00[EUR][1000 genomes]
rs73333173	1.00[EUR][1000 genomes]
rs73333180	1.00[EUR][1000 genomes]
rs73333182	1.00[EUR][1000 genomes]
rs73335009	1.00[EUR][1000 genomes]
rs73339025	1.00[AMR][1000 genomes]
rs73339049	1.00[AMR][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	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	nsv3340	chr20:25160137-25190540	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 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	chr20:25177600-25190400	Weak transcription	HUVEC	blood vessel
2	chr20:25177800-25191600	Weak transcription	NH-A	brain
3	chr20:25178000-25192600	Weak transcription	Fetal Lung	lung
4	chr20:25178200-25187800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr20:25178200-25192000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr20:25178200-25192000	Weak transcription	Aorta	Aorta
7	chr20:25178400-25190400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr20:25178400-25203800	Weak transcription	Small Intestine	intestine
9	chr20:25178400-25203800	Weak transcription	Hela-S3	cervix
10	chr20:25178600-25187400	Weak transcription	Liver	Liver
11	chr20:25178600-25190400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr20:25178600-25190600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr20:25178600-25195600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr20:25178600-25200400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr20:25178600-25212200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr20:25178800-25187600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr20:25179800-25190600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr20:25180000-25187400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr20:25180000-25191800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr20:25180000-25192200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr20:25180000-25207600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr20:25180200-25187800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr20:25180400-25192000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr20:25180600-25191600	Weak transcription	HSMMtube	muscle
25	chr20:25180800-25190600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr20:25180800-25190600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr20:25180800-25191000	Weak transcription	HSMM	muscle
28	chr20:25180800-25191600	Weak transcription	NHDF-Ad	bronchial
29	chr20:25180800-25196000	Weak transcription	Psoas Muscle	Psoas
30	chr20:25180800-25196200	Weak transcription	Fetal Brain Male	brain
31	chr20:25181000-25190400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr20:25181200-25190400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr20:25181400-25190400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr20:25181800-25190600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr20:25181800-25202000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr20:25182000-25190400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr20:25182600-25190400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr20:25184000-25190600	Weak transcription	Colon Smooth Muscle	Colon
39	chr20:25184000-25190600	Weak transcription	Fetal Brain Female	brain
40	chr20:25184200-25188000	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr20:25184200-25188000	Strong transcription	A549	lung
42	chr20:25184200-25190400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr20:25184600-25190400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr20:25184800-25187400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr20:25184800-25190400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr20:25185000-25188800	Strong transcription	Thymus	Thymus
47	chr20:25185000-25190400	Weak transcription	Dnd41	blood
48	chr20:25185000-25193800	Weak transcription	Fetal Kidney	kidney
49	chr20:25185200-25187400	Enhancers	Left Ventricle	heart
50	chr20:25185200-25188200	Strong transcription	HepG2	liver

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