Variant report

Variant	rs2423753
Chromosome Location	chr20:13799949-13799950
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:13799322..13800081-chr20:14035980..14036894,2	MCF-7	breast:
2	chr20:13769074..13771240-chr20:13798879..13801315,2	K562	blood:
3	chr20:13793977..13796033-chr20:13799302..13801878,2	K562	blood:

Variant related genes	Relation type
ENSG00000101247	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs13042637	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1547920	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1999112	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2209993	0.86[ASN][1000 genomes]
rs2209994	0.86[ASN][1000 genomes]
rs2423745	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2423749	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2423750	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3180370	0.93[ASN][1000 genomes]
rs34449907	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34806363	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34901599	0.84[AFR][1000 genomes]
rs35361761	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35632254	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4813142	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4814256	0.82[ASN][1000 genomes]
rs6033819	0.86[ASN][1000 genomes]
rs6033821	0.95[ASN][1000 genomes]
rs6042351	0.86[ASN][1000 genomes]
rs6042362	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6074643	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6074644	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079162	0.82[ASN][1000 genomes]
rs6079165	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6079166	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6079176	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6079178	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6079181	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079182	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6110026	0.82[ASN][1000 genomes]
rs6110035	0.86[ASN][1000 genomes]
rs6134968	0.86[ASN][1000 genomes]
rs62209178	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62209207	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68012295	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13767800-13800600	Weak transcription	Stomach Mucosa	stomach
2	chr20:13769400-13802000	Strong transcription	A549	lung
3	chr20:13780800-13800800	Strong transcription	Placenta	Placenta
4	chr20:13781600-13800000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr20:13783600-13802000	Strong transcription	Dnd41	blood
6	chr20:13788400-13801000	Strong transcription	Fetal Muscle Leg	muscle
7	chr20:13791200-13804800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr20:13792200-13800400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr20:13792400-13803000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr20:13793000-13800200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr20:13793000-13804200	Weak transcription	Psoas Muscle	Psoas
12	chr20:13793000-13805200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr20:13793200-13800600	Weak transcription	Small Intestine	intestine
14	chr20:13793400-13801200	Weak transcription	Hela-S3	cervix
15	chr20:13795600-13804800	Weak transcription	NHLF	lung
16	chr20:13797000-13803200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr20:13797400-13800200	Weak transcription	Fetal Kidney	kidney
18	chr20:13797400-13800800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr20:13797400-13800800	Weak transcription	Gastric	stomach
20	chr20:13797400-13800800	Weak transcription	Pancreas	Pancrea
21	chr20:13797400-13801000	Weak transcription	Ovary	ovary
22	chr20:13797400-13801800	Weak transcription	NH-A	brain
23	chr20:13797400-13802000	Weak transcription	Aorta	Aorta
24	chr20:13797400-13802000	Weak transcription	Brain Angular Gyrus	brain
25	chr20:13797400-13803600	Weak transcription	Fetal Stomach	stomach
26	chr20:13797400-13804600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr20:13797400-13805000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr20:13797400-13807000	Weak transcription	Esophagus	oesophagus
29	chr20:13797400-13820200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr20:13798200-13805000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr20:13798400-13800400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr20:13798400-13802200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr20:13798600-13800800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr20:13798600-13801000	Weak transcription	Colon Smooth Muscle	Colon
35	chr20:13798600-13802200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr20:13798600-13803800	Weak transcription	Fetal Brain Female	brain
37	chr20:13798600-13804200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr20:13798800-13800400	Weak transcription	Colonic Mucosa	Colon
39	chr20:13798800-13800400	Weak transcription	Fetal Lung	lung
40	chr20:13798800-13801600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr20:13798800-13802800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr20:13798800-13803400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr20:13798800-13803600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr20:13798800-13804200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr20:13798800-13804600	Weak transcription	Right Ventricle	heart
46	chr20:13799000-13800600	Weak transcription	Primary B cells from peripheral blood	blood
47	chr20:13799000-13800800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr20:13799000-13802000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr20:13799000-13802000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr20:13799000-13802800	Weak transcription	HMEC	breast

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