Variant report

Variant	rs55793738
Chromosome Location	chr2:20784399-20784400
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20783319..20786192-chr2:20833674..20835720,2	MCF-7	breast:
2	chr2:20777247..20781087-chr2:20782458..20786081,5	K562	blood:
3	chr2:20769124..20771781-chr2:20783924..20785551,2	MCF-7	breast:
4	chr2:20645526..20651779-chr2:20782666..20787622,12	MCF-7	breast:
5	chr2:20783982..20787771-chr2:20790367..20794656,9	K562	blood:
6	chr2:20646487..20649741-chr2:20783299..20785992,4	MCF-7	breast:
7	chr2:20778242..20781356-chr2:20782083..20785108,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143878	Chromatin interaction
ENSG00000231948	Chromatin interaction
ENSG00000228950	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs28488411	0.92[AFR][1000 genomes]
rs28529647	0.92[AFR][1000 genomes]
rs28600892	0.92[AFR][1000 genomes]
rs28642817	0.92[AFR][1000 genomes]
rs55751815	0.81[AFR][1000 genomes]
rs57360378	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58726406	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59300971	0.90[AFR][1000 genomes]
rs59618840	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59771803	0.97[AFR][1000 genomes]
rs60631754	0.81[EUR][1000 genomes]
rs60759855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61272752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62124220	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62124225	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62124226	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62124227	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62124228	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62124229	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62124230	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62124231	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62124232	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62124234	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62125670	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62125672	0.81[EUR][1000 genomes]
rs73916905	0.90[EUR][1000 genomes]
rs73919913	0.89[AFR][1000 genomes]
rs73919915	0.90[AFR][1000 genomes]
rs73919918	0.94[AFR][1000 genomes]
rs73919920	0.97[AFR][1000 genomes]
rs73919921	0.97[AFR][1000 genomes]
rs73919922	0.97[AFR][1000 genomes]
rs73919923	0.96[AFR][1000 genomes]
rs73919924	0.97[AFR][1000 genomes]
rs73919926	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73919928	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73919930	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7564684	0.97[AFR][1000 genomes]
rs7574045	0.97[AFR][1000 genomes]
rs7574289	0.85[AFR][1000 genomes]
rs7588678	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7595132	0.81[AFR][1000 genomes]
rs7601273	0.97[AFR][1000 genomes]
rs896737	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers 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 miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1012037	chr2:20770850-20824893	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535598	chr2:20770850-20824893	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20765800-20786200	Enhancers	HUVEC	blood vessel
2	chr2:20772600-20785800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:20778800-20784800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:20780000-20784400	Weak transcription	Colonic Mucosa	Colon
5	chr2:20780000-20786000	Weak transcription	Small Intestine	intestine
6	chr2:20781600-20785400	Enhancers	Placenta Amnion	Placenta Amnion
7	chr2:20781600-20786000	Enhancers	Brain Hippocampus Middle	brain
8	chr2:20781800-20786000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr2:20781800-20786000	Enhancers	Brain Anterior Caudate	brain
10	chr2:20781800-20786000	Enhancers	Brain Substantia Nigra	brain
11	chr2:20781800-20786200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:20781800-20786800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:20782000-20785400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:20782000-20785800	Enhancers	Brain Angular Gyrus	brain
15	chr2:20782000-20785800	Enhancers	K562	blood
16	chr2:20782000-20786000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:20782000-20786200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:20782000-20786200	Enhancers	Fetal Intestine Small	intestine
19	chr2:20782000-20787400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr2:20782200-20786200	Enhancers	Placenta	Placenta
21	chr2:20782200-20786400	Enhancers	Fetal Stomach	stomach
22	chr2:20782400-20785600	Enhancers	Fetal Intestine Large	intestine
23	chr2:20782400-20785800	Enhancers	Brain Cingulate Gyrus	brain
24	chr2:20782400-20786000	Enhancers	Left Ventricle	heart
25	chr2:20782400-20786000	Enhancers	Pancreas	Pancrea
26	chr2:20782400-20786000	Enhancers	Right Ventricle	heart
27	chr2:20782400-20786400	Enhancers	Right Atrium	heart
28	chr2:20782400-20786400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr2:20782600-20785000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:20782600-20785000	Enhancers	Stomach Mucosa	stomach
31	chr2:20782600-20786000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:20782600-20786000	Enhancers	Spleen	Spleen
33	chr2:20782600-20787800	Enhancers	Adipose Nuclei	Adipose
34	chr2:20782800-20785200	Enhancers	Gastric	stomach
35	chr2:20782800-20785400	Enhancers	HMEC	breast
36	chr2:20782800-20785600	Enhancers	NH-A	brain
37	chr2:20782800-20786000	Enhancers	Lung	lung
38	chr2:20782800-20786200	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr2:20782800-20787400	Enhancers	Fetal Muscle Leg	muscle
40	chr2:20783000-20785800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:20783400-20785000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:20783400-20785400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr2:20783400-20785400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:20783400-20786800	Enhancers	NHDF-Ad	bronchial
45	chr2:20783600-20785000	Enhancers	H9 Cell Line	embryonic stem cell
46	chr2:20783600-20785200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:20783600-20785400	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr2:20783600-20785400	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr2:20783600-20785600	Enhancers	Fetal Kidney	kidney
50	chr2:20783600-20785800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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