Variant report

Variant	rs11667052
Chromosome Location	chr19:57036012-57036013
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11084452	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11671776	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151151	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151254	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12975138	0.80[AMR][1000 genomes]
rs12978999	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.86[MKK][hapmap];0.82[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12980452	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12981892	0.80[AMR][1000 genomes]
rs12981980	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.83[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12986047	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15507	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16987295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16987303	0.94[CEU][hapmap]
rs16987310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.89[MKK][hapmap];0.83[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1939	0.80[AMR][1000 genomes]
rs2074941	0.89[LWK][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs2074942	0.89[LWK][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs2215151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286422	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088221	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34225229	0.80[AMR][1000 genomes]
rs34269477	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35347939	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35664312	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35908973	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36020383	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36062917	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36075900	0.80[AMR][1000 genomes]
rs3813141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813142	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];0.83[TSI][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]
rs4267437	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4570977	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4801334	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs61144294	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62123030	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62124070	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66522479	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7245557	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246507	1.00[CHB][hapmap];0.80[AMR][1000 genomes]
rs7250075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs917407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs960997	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv580387	chr19:57026396-57040070	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11667052	ZFP28	Cis_1M	lymphoblastoid	RTeQTL
rs11667052	AC007228.11	cis	Esophagus Muscularis	GTEx
rs11667052	ZNF471	cis	multi-tissue	Pritchard

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:57022600-57042800	ZNF genes & repeats	Liver	Liver
2	chr19:57022800-57049200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:57023000-57037400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr19:57024400-57038800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr19:57025600-57038200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr19:57025600-57049200	ZNF genes & repeats	Adipose Nuclei	Adipose
7	chr19:57026000-57040200	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
8	chr19:57027200-57038600	ZNF genes & repeats	Ovary	ovary
9	chr19:57027400-57040800	ZNF genes & repeats	Brain Hippocampus Middle	brain
10	chr19:57029000-57036800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:57029000-57037400	ZNF genes & repeats	Fetal Muscle Leg	muscle
12	chr19:57029000-57039200	ZNF genes & repeats	Left Ventricle	heart
13	chr19:57029000-57041600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:57029200-57041000	ZNF genes & repeats	Brain Cingulate Gyrus	brain
15	chr19:57029200-57042600	ZNF genes & repeats	Brain Substantia Nigra	brain
16	chr19:57029400-57037800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
17	chr19:57029600-57038200	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:57029600-57038200	ZNF genes & repeats	Colon Smooth Muscle	Colon
19	chr19:57029600-57039400	ZNF genes & repeats	Fetal Brain Female	brain
20	chr19:57029600-57041800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
21	chr19:57029600-57046200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
22	chr19:57029800-57038800	ZNF genes & repeats	Brain Anterior Caudate	brain
23	chr19:57030000-57038200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
24	chr19:57030400-57036800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:57030600-57036600	ZNF genes & repeats	Pancreas	Pancrea
26	chr19:57030600-57037000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
27	chr19:57030600-57039600	ZNF genes & repeats	Brain Germinal Matrix	brain
28	chr19:57030800-57039200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
29	chr19:57031200-57041000	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
30	chr19:57031800-57038800	ZNF genes & repeats	Right Ventricle	heart
31	chr19:57032000-57036600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr19:57033000-57039600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
33	chr19:57033200-57037600	ZNF genes & repeats	Fetal Brain Male	brain
34	chr19:57033400-57037000	ZNF genes & repeats	Fetal Heart	heart
35	chr19:57033400-57037200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
36	chr19:57033400-57038000	ZNF genes & repeats	Psoas Muscle	Psoas
37	chr19:57033800-57036200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr19:57033800-57038400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
39	chr19:57034200-57037000	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
40	chr19:57034600-57038000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
41	chr19:57034800-57039400	ZNF genes & repeats	Brain Angular Gyrus	brain
42	chr19:57035200-57036600	ZNF genes & repeats	Placenta	Placenta
43	chr19:57035200-57037000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
44	chr19:57035200-57038000	ZNF genes & repeats	Fetal Lung	lung
45	chr19:57035200-57038200	ZNF genes & repeats	Gastric	stomach
46	chr19:57035200-57039200	ZNF genes & repeats	Rectal Smooth Muscle	rectum
47	chr19:57035600-57036400	Weak transcription	Aorta	Aorta
48	chr19:57035600-57038200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr19:57036000-57036600	ZNF genes & repeats	Placenta Amnion	Placenta Amnion
50	chr19:57036000-57037000	ZNF genes & repeats	NH-A	brain

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