Variant report

Variant	rs55789595
Chromosome Location	chr12:48454681-48454682
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48438521..48441289-chr12:48453663..48455764,2	K562	blood:
2	chr12:48404615..48406562-chr12:48453440..48456086,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258203	Chromatin interaction
ENSG00000257985	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs55759881	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55991805	0.83[AMR][1000 genomes]
rs57539024	0.83[AMR][1000 genomes]
rs58148022	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58373242	1.00[AMR][1000 genomes]
rs59051221	0.83[AMR][1000 genomes]
rs59643562	0.83[AMR][1000 genomes]
rs59787033	0.83[AMR][1000 genomes]
rs59896935	0.83[AMR][1000 genomes]
rs60001451	0.83[AMR][1000 genomes]
rs60316794	0.83[AMR][1000 genomes]
rs61356079	0.86[AFR][1000 genomes]
rs61558457	0.83[AMR][1000 genomes]
rs61750873	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7316275	0.83[AMR][1000 genomes]
rs74086781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74086968	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74086984	0.83[AMR][1000 genomes]
rs74089112	0.83[AMR][1000 genomes]
rs74089120	0.83[AMR][1000 genomes]
rs74089127	0.83[AMR][1000 genomes]
rs74089135	0.83[AMR][1000 genomes]
rs74089149	0.83[AMR][1000 genomes]
rs74089151	0.83[AMR][1000 genomes]
rs74089154	0.83[AMR][1000 genomes]
rs74089161	0.83[AMR][1000 genomes]
rs74089171	0.83[AMR][1000 genomes]
rs74089530	0.98[AFR][1000 genomes]
rs74089540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089548	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089549	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089550	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48431800-48456600	Weak transcription	NHLF	lung
2	chr12:48432000-48463400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:48435200-48476200	Weak transcription	Stomach Mucosa	stomach
5	chr12:48435400-48457200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:48437200-48489000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:48439200-48456800	Weak transcription	HMEC	breast
8	chr12:48439200-48468000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:48439600-48455400	Weak transcription	Colonic Mucosa	Colon
10	chr12:48440000-48457200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr12:48441200-48457000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr12:48441400-48482600	Weak transcription	Small Intestine	intestine
13	chr12:48441600-48468000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:48443000-48478800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:48444200-48474600	Weak transcription	Gastric	stomach
16	chr12:48444800-48468000	Weak transcription	Spleen	Spleen
17	chr12:48449400-48464400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:48452000-48460200	Strong transcription	Hela-S3	cervix
19	chr12:48452000-48468600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:48452000-48468800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:48452000-48468800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:48452000-48469400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:48452200-48454800	ZNF genes & repeats	Dnd41	blood
24	chr12:48452200-48455200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:48452200-48459600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:48452200-48459600	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr12:48452200-48459600	Strong transcription	NHDF-Ad	bronchial
28	chr12:48452200-48460000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr12:48452200-48460600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr12:48452200-48461200	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr12:48452200-48461600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:48452200-48468600	Strong transcription	NH-A	brain
33	chr12:48452200-48468800	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:48452200-48469000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr12:48452200-48469600	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr12:48452200-48470000	Strong transcription	Placenta	Placenta
37	chr12:48452400-48455200	ZNF genes & repeats	Primary B cells from cord blood	blood
38	chr12:48452400-48459400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr12:48452400-48459600	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr12:48452400-48459600	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr12:48452400-48459600	Strong transcription	Osteobl	bone
42	chr12:48452400-48459800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr12:48452400-48460000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr12:48452400-48460600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:48452400-48460600	Strong transcription	Left Ventricle	heart
46	chr12:48452400-48461400	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr12:48452400-48461600	Strong transcription	Fetal Intestine Large	intestine
48	chr12:48452400-48463200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr12:48452400-48468800	Strong transcription	Adipose Nuclei	Adipose
50	chr12:48452400-48468800	Strong transcription	Duodenum Mucosa	Duodenum

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