Variant report

Variant	rs2423754
Chromosome Location	chr20:13803263-13803264
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	chr20:13802809..13804959-chr20:13816755..13818669,2	K562	blood:
2	chr20:13796937..13798813-chr20:13802181..13804094,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101247	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2094652	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2327796	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs243917	1.00[EUR][1000 genomes]
rs34901599	1.00[AMR][1000 genomes]
rs4239710	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4814255	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4814257	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4814259	0.85[AFR][1000 genomes]
rs6033822	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042326	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042334	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042344	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6074639	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6079175	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13791200-13804800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:13793000-13804200	Weak transcription	Psoas Muscle	Psoas
3	chr20:13793000-13805200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr20:13795600-13804800	Weak transcription	NHLF	lung
5	chr20:13797400-13803600	Weak transcription	Fetal Stomach	stomach
6	chr20:13797400-13804600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr20:13797400-13805000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr20:13797400-13807000	Weak transcription	Esophagus	oesophagus
9	chr20:13797400-13820200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr20:13798200-13805000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr20:13798600-13803800	Weak transcription	Fetal Brain Female	brain
12	chr20:13798600-13804200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr20:13798800-13803400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr20:13798800-13803600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr20:13798800-13804200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr20:13798800-13804600	Weak transcription	Right Ventricle	heart
17	chr20:13799000-13804000	Weak transcription	HSMM	muscle
18	chr20:13799000-13804800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr20:13799400-13803400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr20:13799400-13803600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr20:13799400-13803800	Weak transcription	NHEK	skin
22	chr20:13799400-13804200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr20:13799400-13804600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr20:13799400-13805000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr20:13799400-13805200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr20:13799400-13805400	Weak transcription	Primary T cells from cord blood	blood
27	chr20:13799400-13807200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr20:13799600-13803400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr20:13799600-13803600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr20:13799600-13803800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr20:13799600-13804000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr20:13799600-13804000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr20:13799600-13804600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr20:13799600-13804800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr20:13799600-13804800	Weak transcription	HepG2	liver
36	chr20:13799600-13805000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr20:13799600-13807000	Weak transcription	Left Ventricle	heart
38	chr20:13799600-13808000	Weak transcription	Brain Hippocampus Middle	brain
39	chr20:13799800-13804000	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr20:13799800-13804400	Weak transcription	Fetal Intestine Large	intestine
41	chr20:13799800-13807800	Weak transcription	Brain Anterior Caudate	brain
42	chr20:13800000-13803600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr20:13801000-13804200	Weak transcription	Fetal Muscle Leg	muscle
44	chr20:13802000-13804800	Weak transcription	Dnd41	blood
45	chr20:13802200-13803600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr20:13802200-13804400	Weak transcription	HSMMtube	muscle
47	chr20:13802400-13803600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr20:13802400-13803800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr20:13802400-13804000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr20:13802800-13803400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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