Variant report

Variant	rs204553
Chromosome Location	chr19:44940880-44940881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1734622	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1865385	1.00[ASN][1000 genomes]
rs204527	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204529	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204530	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204532	1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204542	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204548	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204550	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204554	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs204556	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2571041	1.00[ASN][1000 genomes]
rs2571053	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2571059	1.00[ASN][1000 genomes]
rs2686756	1.00[ASN][1000 genomes]
rs2686757	1.00[ASN][1000 genomes]
rs2686769	1.00[ASN][1000 genomes]
rs431273	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62118147	1.00[ASN][1000 genomes]
rs629579	1.00[ASN][1000 genomes]
rs8107008	1.00[CHB][hapmap]
rs8110499	0.92[EUR][1000 genomes]
rs930462	1.00[CHB][hapmap]
rs954314	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv2763206	chr19:44885379-44941728	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv2756827	chr19:44894102-44947444	Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2758764	chr19:44894102-44947444	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs204553	ZNF180	cis	Muscle Skeletal	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44928000-44943600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
2	chr19:44928200-44941000	ZNF genes & repeats	Liver	Liver
3	chr19:44928200-44941000	ZNF genes & repeats	Ovary	ovary
4	chr19:44928200-44943400	ZNF genes & repeats	Adipose Nuclei	Adipose
5	chr19:44928400-44951800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:44929200-44945400	ZNF genes & repeats	Brain Germinal Matrix	brain
7	chr19:44929400-44941000	ZNF genes & repeats	Fetal Brain Female	brain
8	chr19:44931800-44941000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
9	chr19:44931800-44941600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr19:44932000-44941000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
11	chr19:44932000-44943400	ZNF genes & repeats	Fetal Lung	lung
12	chr19:44932000-44953200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
13	chr19:44932200-44941000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr19:44932200-44941000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
15	chr19:44932200-44941000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:44932200-44941000	ZNF genes & repeats	Left Ventricle	heart
17	chr19:44932200-44943400	ZNF genes & repeats	A549	lung
18	chr19:44932200-44943600	ZNF genes & repeats	Stomach Smooth Muscle	stomach
19	chr19:44932400-44941000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr19:44932400-44941000	ZNF genes & repeats	Aorta	Aorta
21	chr19:44932400-44941000	ZNF genes & repeats	Fetal Stomach	stomach
22	chr19:44932600-44941000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr19:44932600-44941000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr19:44932600-44941000	ZNF genes & repeats	Fetal Intestine Small	intestine
25	chr19:44933800-44941200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr19:44934600-44950800	Weak transcription	Hela-S3	cervix
27	chr19:44935200-44941000	ZNF genes & repeats	Brain Anterior Caudate	brain
28	chr19:44935800-44942200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
29	chr19:44936000-44951400	Weak transcription	Fetal Heart	heart
30	chr19:44936400-44952000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:44937200-44941000	ZNF genes & repeats	Primary T cells from cord blood	blood
32	chr19:44937400-44946400	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr19:44937400-44951800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr19:44937800-44942600	Weak transcription	HSMMtube	muscle
35	chr19:44938400-44941000	ZNF genes & repeats	Lung	lung
36	chr19:44938400-44951800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:44938600-44941000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr19:44938600-44941000	ZNF genes & repeats	Rectal Smooth Muscle	rectum
39	chr19:44938600-44941000	Strong transcription	Right Ventricle	heart
40	chr19:44938600-44941200	ZNF genes & repeats	Psoas Muscle	Psoas
41	chr19:44938600-44946600	Weak transcription	HSMM	muscle
42	chr19:44938800-44942400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr19:44938800-44945800	Weak transcription	NHLF	lung
44	chr19:44938800-44946400	Weak transcription	Fetal Kidney	kidney
45	chr19:44938800-44951600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr19:44939000-44945400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr19:44939000-44946000	Weak transcription	NH-A	brain
48	chr19:44939000-44948400	Weak transcription	NHEK	skin
49	chr19:44939400-44941000	ZNF genes & repeats	Pancreas	Pancrea
50	chr19:44940000-44941000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links