Variant report

Variant	rs4803680
Chromosome Location	chr19:44609293-44609294
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:44609210-44609324	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ZNF224	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10410306	0.84[EUR][1000 genomes]
rs10420143	0.84[EUR][1000 genomes]
rs2061332	0.86[CHB][hapmap]
rs2061333	0.86[CHB][hapmap]
rs2068061	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2284978	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2300962	0.81[ASN][1000 genomes]
rs28446946	0.85[EUR][1000 genomes]
rs28539456	0.85[EUR][1000 genomes]
rs3172	0.90[CHB][hapmap]
rs3746319	0.86[CHB][hapmap]
rs4239529	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4429390	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4459653	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4508518	0.82[CHB][hapmap]
rs4802206	0.84[EUR][1000 genomes]
rs4803674	0.83[CEU][hapmap]
rs4803676	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803677	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803681	0.86[CHB][hapmap]
rs6509141	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7249827	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250004	0.84[EUR][1000 genomes]
rs7250005	0.82[EUR][1000 genomes]
rs7250076	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7250171	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7508149	0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs8101657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104573	0.84[EUR][1000 genomes]
rs8105860	0.84[EUR][1000 genomes]
rs8113487	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8113750	0.85[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4803680	ZNF223	cis	Thyroid	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44599600-44610600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:44599600-44611000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:44599800-44610400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:44600000-44610400	Weak transcription	Stomach Mucosa	stomach
5	chr19:44600400-44610400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:44600400-44610600	Strong transcription	HSMM	muscle
7	chr19:44600400-44616200	ZNF genes & repeats	Liver	Liver
8	chr19:44600800-44610400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr19:44600800-44610400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr19:44600800-44610600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr19:44600800-44610600	Strong transcription	Skeletal Muscle Male	skeletal muscle
12	chr19:44600800-44612800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr19:44600800-44614000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:44600800-44614600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:44601000-44609400	Strong transcription	Brain Inferior Temporal Lobe	brain
16	chr19:44601000-44610600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr19:44601000-44611600	Strong transcription	Fetal Thymus	thymus
18	chr19:44601400-44609400	Strong transcription	Brain Hippocampus Middle	brain
19	chr19:44601400-44611000	Strong transcription	Placenta	Placenta
20	chr19:44601800-44609400	Strong transcription	Brain Cingulate Gyrus	brain
21	chr19:44602000-44609400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr19:44602000-44610400	Strong transcription	Dnd41	blood
23	chr19:44604200-44610400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:44604200-44610400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr19:44604200-44613000	ZNF genes & repeats	Adipose Nuclei	Adipose
26	chr19:44604400-44609400	ZNF genes & repeats	Aorta	Aorta
27	chr19:44604600-44609600	Strong transcription	HUVEC	blood vessel
28	chr19:44604600-44610400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr19:44604600-44610400	Strong transcription	NH-A	brain
30	chr19:44604600-44612800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
31	chr19:44604800-44612400	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr19:44604800-44616000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
33	chr19:44605000-44610600	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr19:44605200-44609400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr19:44605200-44609400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
36	chr19:44605200-44614600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr19:44605400-44609400	Strong transcription	NHLF	lung
38	chr19:44605600-44609400	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
39	chr19:44605600-44610200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr19:44605800-44612600	ZNF genes & repeats	Primary T cells from cord blood	blood
41	chr19:44605800-44613000	ZNF genes & repeats	Fetal Lung	lung
42	chr19:44606400-44609600	Strong transcription	Stomach Smooth Muscle	stomach
43	chr19:44606400-44610600	Weak transcription	HepG2	liver
44	chr19:44606600-44616400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
45	chr19:44606800-44610400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr19:44607000-44612000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
47	chr19:44607000-44612600	ZNF genes & repeats	GM12878-XiMat	blood
48	chr19:44607000-44612800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
49	chr19:44607000-44612800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
50	chr19:44607000-44613000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung

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