Variant report

Variant	rs7250221
Chromosome Location	chr19:44992664-44992665
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1865385	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1897821	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1897824	0.93[EUR][1000 genomes]
rs2117384	0.96[EUR][1000 genomes]
rs2461534	0.92[EUR][1000 genomes]
rs2571040	0.92[EUR][1000 genomes]
rs2571041	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2571046	0.92[EUR][1000 genomes]
rs2571048	0.92[EUR][1000 genomes]
rs2571049	0.92[EUR][1000 genomes]
rs2571050	0.97[EUR][1000 genomes]
rs2571053	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2571059	0.90[EUR][1000 genomes]
rs2571115	0.81[EUR][1000 genomes]
rs2571116	0.84[EUR][1000 genomes]
rs2686756	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2686757	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2686758	0.92[EUR][1000 genomes]
rs2686762	0.97[EUR][1000 genomes]
rs2686769	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62118145	0.81[EUR][1000 genomes]
rs62118147	0.82[EUR][1000 genomes]
rs629579	0.90[EUR][1000 genomes]
rs926020	0.92[EUR][1000 genomes]
rs954314	0.98[AMR][1000 genomes];0.98[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	nsv912112	chr19:44853707-45011727	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv912114	chr19:44858776-45002563	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1061350	chr19:44869075-45035469	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv912115	chr19:44957508-44995990	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7250221	ZNF180	cis	Muscle Skeletal	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44967200-44992800	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr19:44977200-44992800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr19:44978000-44992800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr19:44978400-44993600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:44978800-45003400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
6	chr19:44983400-44992800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
7	chr19:44989000-44997000	Weak transcription	Hela-S3	cervix
8	chr19:44989200-44996800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:44990400-44995000	Weak transcription	Osteobl	bone
10	chr19:44990600-44992800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr19:44990600-44992800	ZNF genes & repeats	Aorta	Aorta
12	chr19:44990600-44993000	ZNF genes & repeats	Ovary	ovary
13	chr19:44990800-44992800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr19:44990800-44992800	ZNF genes & repeats	Esophagus	oesophagus
15	chr19:44990800-44992800	ZNF genes & repeats	Fetal Stomach	stomach
16	chr19:44990800-44992800	ZNF genes & repeats	Left Ventricle	heart
17	chr19:44990800-44993600	Weak transcription	K562	blood
18	chr19:44991600-44992800	ZNF genes & repeats	Pancreas	Pancrea
19	chr19:44991600-44993200	ZNF genes & repeats	Lung	lung
20	chr19:44991800-44994000	Weak transcription	HepG2	liver
21	chr19:44991800-44994200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr19:44991800-44994400	Weak transcription	Colon Smooth Muscle	Colon
23	chr19:44991800-44994800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr19:44991800-44994800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr19:44991800-44995000	Weak transcription	HSMM	muscle
26	chr19:44991800-44995200	Weak transcription	HSMMtube	muscle
27	chr19:44991800-44996000	Weak transcription	Fetal Heart	heart
28	chr19:44992000-44993200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr19:44992000-44994000	Weak transcription	Brain Germinal Matrix	brain
30	chr19:44992000-44994000	Weak transcription	Fetal Kidney	kidney
31	chr19:44992000-44994000	Weak transcription	A549	lung
32	chr19:44992000-44994000	Weak transcription	GM12878-XiMat	blood
33	chr19:44992000-44994200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr19:44992000-44994200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr19:44992000-44994200	Weak transcription	Primary T cells from cord blood	blood
36	chr19:44992000-44994200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr19:44992000-44994200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr19:44992000-44994400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr19:44992000-44994400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr19:44992000-44994400	Weak transcription	Right Ventricle	heart
41	chr19:44992000-44994800	Weak transcription	NHEK	skin
42	chr19:44992000-44995000	Weak transcription	Brain Angular Gyrus	brain
43	chr19:44992000-44995200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:44992000-44995200	Weak transcription	HUVEC	blood vessel
45	chr19:44992200-44994000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr19:44992200-44994000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr19:44992200-44994000	Weak transcription	Brain Anterior Caudate	brain
48	chr19:44992200-44994000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr19:44992200-44994000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr19:44992200-44994000	Weak transcription	Fetal Brain Female	brain

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