Variant report

Variant	rs55820056
Chromosome Location	chr12:48497737-48497738
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48497572..48499249-chr12:48549769..48551418,2	MCF-7	breast:
2	chr12:48492802..48495479-chr12:48497432..48499214,2	K562	blood:
3	chr12:48496939..48501728-chr12:48549612..48553634,6	MCF-7	breast:
4	chr12:48497586..48502171-chr12:48511099..48514258,8	MCF-7	breast:
5	chr12:48495831..48503326-chr12:48548997..48555180,8	K562	blood:
6	chr12:48497262..48501671-chr12:48511273..48513832,5	K562	blood:
7	chr12:48496389..48500489-chr12:48511491..48515053,4	K562	blood:

Variant related genes	Relation type
ENSG00000152556	Chromatin interaction
ENSG00000258051	Chromatin interaction
ENSG00000177981	Chromatin interaction
ENSG00000079387	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10128967	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10128968	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506279	1.00[ASN][1000 genomes]
rs11835938	1.00[ASN][1000 genomes]
rs12301562	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12316682	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2450995	1.00[ASN][1000 genomes]
rs41291959	0.82[EUR][1000 genomes]
rs41291963	1.00[ASN][1000 genomes]
rs41291967	1.00[ASN][1000 genomes]
rs55707383	0.83[EUR][1000 genomes]
rs55953382	0.83[EUR][1000 genomes]
rs56049209	0.82[EUR][1000 genomes]
rs56345199	0.87[AMR][1000 genomes]
rs57956448	1.00[ASN][1000 genomes]
rs58317398	1.00[ASN][1000 genomes]
rs60209369	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60679254	1.00[ASN][1000 genomes]
rs73304917	1.00[ASN][1000 genomes]
rs74089110	1.00[ASN][1000 genomes]
rs74089159	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74089163	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630296	0.82[EUR][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	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
2	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
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55820056	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:48453000-48498200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:48468600-48498400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:48468800-48498200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:48475000-48498200	Weak transcription	Psoas Muscle	Psoas
6	chr12:48476800-48498400	Weak transcription	Fetal Brain Male	brain
7	chr12:48477200-48498200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:48477400-48498400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:48479400-48498200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:48479400-48498200	Weak transcription	Brain Angular Gyrus	brain
11	chr12:48479400-48498400	Weak transcription	Aorta	Aorta
12	chr12:48479600-48498000	Weak transcription	NHEK	skin
13	chr12:48480400-48498200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr12:48482800-48498200	Weak transcription	NHDF-Ad	bronchial
15	chr12:48483000-48498200	Weak transcription	NH-A	brain
16	chr12:48483000-48498400	Weak transcription	HSMMtube	muscle
17	chr12:48483200-48498200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:48483200-48498200	Weak transcription	HepG2	liver
19	chr12:48483200-48498400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr12:48483200-48499200	Weak transcription	Small Intestine	intestine
21	chr12:48483400-48498200	Weak transcription	NHLF	lung
22	chr12:48484800-48498200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:48485000-48498200	Weak transcription	Spleen	Spleen
24	chr12:48486200-48499000	Weak transcription	Gastric	stomach
25	chr12:48486400-48497800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr12:48488000-48498200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr12:48488200-48498200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:48488200-48498200	Weak transcription	Lung	lung
29	chr12:48488200-48498200	Weak transcription	Pancreas	Pancrea
30	chr12:48488200-48498400	Weak transcription	Brain Substantia Nigra	brain
31	chr12:48488200-48499200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:48488400-48498200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:48488400-48498400	Weak transcription	Right Ventricle	heart
34	chr12:48489000-48498200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr12:48489600-48498400	Weak transcription	Left Ventricle	heart
36	chr12:48489600-48499000	Weak transcription	Esophagus	oesophagus
37	chr12:48489800-48498200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:48489800-48498200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr12:48489800-48498200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:48489800-48498400	Weak transcription	Thymus	Thymus
41	chr12:48490000-48498400	Weak transcription	Colonic Mucosa	Colon
42	chr12:48490200-48498200	Weak transcription	Brain Germinal Matrix	brain
43	chr12:48490200-48498200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr12:48490200-48498200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr12:48490200-48498200	Weak transcription	HUVEC	blood vessel
46	chr12:48490600-48499000	Weak transcription	Ovary	ovary
47	chr12:48491400-48498200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr12:48491400-48498200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr12:48491400-48498200	Weak transcription	Fetal Intestine Large	intestine
50	chr12:48491600-48498000	Weak transcription	HMEC	breast

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