Variant report

Variant	rs12979383
Chromosome Location	chr19:57079997-57079998
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10405702	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10406660	0.87[ASN][1000 genomes]
rs10408033	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10409531	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10410277	0.98[ASN][1000 genomes]
rs10412249	1.00[ASN][1000 genomes]
rs10413682	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10415256	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10419789	1.00[ASN][1000 genomes]
rs10421285	1.00[ASN][1000 genomes]
rs10424437	0.96[ASN][1000 genomes]
rs10425965	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10426619	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10427145	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1052280	0.87[ASN][1000 genomes]
rs11084454	0.98[ASN][1000 genomes]
rs11672822	0.94[EUR][1000 genomes]
rs12104204	1.00[ASN][1000 genomes]
rs12104288	1.00[ASN][1000 genomes]
rs12975138	0.96[EUR][1000 genomes]
rs12980452	0.94[EUR][1000 genomes]
rs12981572	1.00[ASN][1000 genomes]
rs12981652	0.94[EUR][1000 genomes]
rs12981892	0.96[EUR][1000 genomes]
rs12982632	0.94[EUR][1000 genomes]
rs1939	0.96[EUR][1000 genomes]
rs2024396	0.86[ASN][1000 genomes]
rs2215929	0.94[EUR][1000 genomes]
rs28428635	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28668141	0.98[ASN][1000 genomes]
rs2869896	0.84[ASN][1000 genomes]
rs2904241	0.97[ASN][1000 genomes]
rs34225229	0.96[EUR][1000 genomes]
rs34760888	0.93[EUR][1000 genomes]
rs36075900	0.96[EUR][1000 genomes]
rs4401145	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4570977	0.94[EUR][1000 genomes]
rs4801174	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4801335	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4801337	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4801339	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4801343	0.98[ASN][1000 genomes]
rs56069810	0.94[EUR][1000 genomes]
rs62124114	0.92[EUR][1000 genomes]
rs7246507	0.96[EUR][1000 genomes]
rs7252022	0.98[ASN][1000 genomes]
rs7252934	0.98[ASN][1000 genomes]
rs7253371	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7253545	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7254001	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7258886	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7259161	0.98[ASN][1000 genomes]
rs7259577	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7259608	0.98[ASN][1000 genomes]
rs7259741	0.98[ASN][1000 genomes]
rs741252	0.98[ASN][1000 genomes]
rs741253	0.94[EUR][1000 genomes]
rs759331	0.98[ASN][1000 genomes]
rs764999	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs765000	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8101497	0.87[ASN][1000 genomes]
rs8106879	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8108667	0.98[ASN][1000 genomes]
rs8110403	0.94[EUR][1000 genomes]
rs9916995	0.98[ASN][1000 genomes]
rs995934	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
7	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
8	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
9	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
10	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12979383	AC007228.11	cis	Esophagus Muscularis	GTEx
rs12979383	ZFP28	Cis_1M	lymphoblastoid	RTeQTL
rs12979383	ZFP28	cis	Whole Blood	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:57077400-57080000	ZNF genes & repeats	GM12878-XiMat	blood
2	chr19:57077600-57082600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr19:57077800-57080000	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr19:57078000-57080000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr19:57078000-57080000	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr19:57078000-57080000	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr19:57078000-57080000	Active TSS	HSMMtube	muscle
8	chr19:57078000-57080000	Active TSS	NHLF	lung
9	chr19:57078200-57080200	Active TSS	NHDF-Ad	bronchial
10	chr19:57078400-57080000	Active TSS	Brain Cingulate Gyrus	brain
11	chr19:57078600-57080000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr19:57079000-57080000	Flanking Active TSS	Fetal Brain Male	brain
13	chr19:57079200-57080000	Flanking Active TSS	Fetal Brain Female	brain
14	chr19:57079200-57080000	Flanking Active TSS	Left Ventricle	heart
15	chr19:57079200-57080000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr19:57079200-57080000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr19:57079200-57080000	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr19:57079200-57080200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:57079200-57082600	ZNF genes & repeats	HSMM	muscle
20	chr19:57079200-57082800	ZNF genes & repeats	A549	lung
21	chr19:57079200-57082800	ZNF genes & repeats	HMEC	breast
22	chr19:57079200-57090000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr19:57079200-57090200	ZNF genes & repeats	Dnd41	blood
24	chr19:57079200-57093400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:57079400-57080000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr19:57079400-57080000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr19:57079400-57080000	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr19:57079400-57080000	Flanking Active TSS	Colon Smooth Muscle	Colon
29	chr19:57079400-57080000	Flanking Active TSS	Fetal Heart	heart
30	chr19:57079400-57080000	Flanking Active TSS	Right Ventricle	heart
31	chr19:57079400-57080200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
32	chr19:57079400-57080600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
33	chr19:57079400-57082800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
34	chr19:57079400-57083600	ZNF genes & repeats	Fetal Intestine Small	intestine
35	chr19:57079400-57083600	ZNF genes & repeats	NHEK	skin
36	chr19:57079400-57084000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr19:57079400-57086800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
38	chr19:57079400-57092800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:57079600-57080000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr19:57079600-57080000	Active TSS	Pancreas	Pancrea
41	chr19:57079600-57080400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr19:57079600-57080600	Weak transcription	Aorta	Aorta
43	chr19:57079600-57080600	Weak transcription	Fetal Thymus	thymus
44	chr19:57079600-57080600	Weak transcription	Ovary	ovary
45	chr19:57079600-57080800	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr19:57079600-57081000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr19:57079600-57081000	Weak transcription	Fetal Stomach	stomach
48	chr19:57079600-57081000	Weak transcription	Gastric	stomach
49	chr19:57079600-57082600	ZNF genes & repeats	Colonic Mucosa	Colon
50	chr19:57079600-57084600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links