Variant report

Variant	rs4801172
Chromosome Location	chr19:57051287-57051288
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1029709	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10406304	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12979404	0.94[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801170	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73629994	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8101060	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8107062	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs917406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS 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	88 gene(s)	inside rSNPs	diseases
5	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv580385	chr19:56918598-57072433	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv580386	chr19:56924761-57072433	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv1055357	chr19:56933632-57190007	ZNF genes & repeats Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	nsv912518	chr19:56995737-57109821	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv912519	chr19:57020754-57065189	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
13	nsv1062806	chr19:57050734-57191914	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers 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 target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4801172	ZFP28	Cis_1M	lymphoblastoid	RTeQTL
rs4801172	ZNF470	cis	multi-tissue	Pritchard
rs4801172	ZNF71	cis	lymphoblastoid	seeQTL
rs4801172	ZNF837	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:57047400-57077800	ZNF genes & repeats	Liver	Liver
2	chr19:57048800-57051400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
3	chr19:57048800-57051600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
4	chr19:57048800-57053000	ZNF genes & repeats	Placenta	Placenta
5	chr19:57048800-57053000	ZNF genes & repeats	HSMM	muscle
6	chr19:57048800-57053800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr19:57049000-57051400	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr19:57049200-57051400	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr19:57049400-57051400	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr19:57049600-57051400	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr19:57049600-57051400	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr19:57049600-57051400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr19:57049600-57051400	Active TSS	HSMMtube	muscle
14	chr19:57049600-57052000	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr19:57050400-57051400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:57050600-57051400	Flanking Active TSS	Fetal Brain Female	brain
17	chr19:57050600-57051400	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr19:57050600-57053000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
19	chr19:57050600-57059400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:57050600-57062800	ZNF genes & repeats	A549	lung
21	chr19:57050800-57051400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr19:57050800-57051400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr19:57050800-57051400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
24	chr19:57050800-57051400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr19:57050800-57051400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr19:57050800-57051400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:57050800-57051400	Flanking Active TSS	Brain Germinal Matrix	brain
28	chr19:57050800-57051400	Flanking Active TSS	Fetal Brain Male	brain
29	chr19:57050800-57054000	ZNF genes & repeats	Fetal Intestine Small	intestine
30	chr19:57050800-57055000	ZNF genes & repeats	Lung	lung
31	chr19:57050800-57063000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
32	chr19:57050800-57067000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:57051000-57051400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr19:57051000-57051400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:57051000-57051400	Genic enhancers	Primary B cells from peripheral blood	blood
36	chr19:57051000-57051400	Enhancers	Left Ventricle	heart
37	chr19:57051000-57051400	Flanking Active TSS	NHEK	skin
38	chr19:57051000-57051600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:57051000-57051600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:57051000-57051600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:57051000-57051600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr19:57051000-57051600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr19:57051000-57051600	Enhancers	Right Atrium	heart
44	chr19:57051000-57051600	Enhancers	Thymus	Thymus
45	chr19:57051000-57052200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr19:57051000-57052200	Weak transcription	Esophagus	oesophagus
47	chr19:57051000-57052200	Weak transcription	Fetal Intestine Large	intestine
48	chr19:57051000-57052200	Weak transcription	Gastric	stomach
49	chr19:57051000-57052200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr19:57051000-57052400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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