Variant report

Variant	rs16987303
Chromosome Location	chr19:57037103-57037104
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZFP28-2	chr19:57037069-57037390	NONHSAT068165

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11667052	0.94[CEU][hapmap]
rs11667653	1.00[ASN][1000 genomes]
rs12151151	0.94[CEU][hapmap]
rs12978999	1.00[CEU][hapmap]
rs12980452	0.81[CEU][hapmap]
rs12981980	0.84[CEU][hapmap]
rs1468773	1.00[ASN][1000 genomes]
rs16987295	0.94[CEU][hapmap]
rs16987310	0.94[CEU][hapmap]
rs2215151	0.94[CEU][hapmap]
rs3813141	0.94[CEU][hapmap]
rs3813143	0.94[CEU][hapmap]
rs7250075	0.94[CEU][hapmap]
rs73059451	1.00[ASN][1000 genomes]
rs8110306	0.94[CEU][hapmap]
rs917407	0.94[CEU][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16987303	ZFP28	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

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	chr19:57029000-57037400	ZNF genes & repeats	Fetal Muscle Leg	muscle
11	chr19:57029000-57039200	ZNF genes & repeats	Left Ventricle	heart
12	chr19:57029000-57041600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr19:57029200-57041000	ZNF genes & repeats	Brain Cingulate Gyrus	brain
14	chr19:57029200-57042600	ZNF genes & repeats	Brain Substantia Nigra	brain
15	chr19:57029400-57037800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
16	chr19:57029600-57038200	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
17	chr19:57029600-57038200	ZNF genes & repeats	Colon Smooth Muscle	Colon
18	chr19:57029600-57039400	ZNF genes & repeats	Fetal Brain Female	brain
19	chr19:57029600-57041800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
20	chr19:57029600-57046200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
21	chr19:57029800-57038800	ZNF genes & repeats	Brain Anterior Caudate	brain
22	chr19:57030000-57038200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
23	chr19:57030600-57039600	ZNF genes & repeats	Brain Germinal Matrix	brain
24	chr19:57030800-57039200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
25	chr19:57031200-57041000	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
26	chr19:57031800-57038800	ZNF genes & repeats	Right Ventricle	heart
27	chr19:57033000-57039600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
28	chr19:57033200-57037600	ZNF genes & repeats	Fetal Brain Male	brain
29	chr19:57033400-57037200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
30	chr19:57033400-57038000	ZNF genes & repeats	Psoas Muscle	Psoas
31	chr19:57033800-57038400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
32	chr19:57034600-57038000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
33	chr19:57034800-57039400	ZNF genes & repeats	Brain Angular Gyrus	brain
34	chr19:57035200-57038000	ZNF genes & repeats	Fetal Lung	lung
35	chr19:57035200-57038200	ZNF genes & repeats	Gastric	stomach
36	chr19:57035200-57039200	ZNF genes & repeats	Rectal Smooth Muscle	rectum
37	chr19:57035600-57038200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr19:57036000-57037200	ZNF genes & repeats	HSMM	muscle
39	chr19:57036000-57037400	ZNF genes & repeats	Fetal Kidney	kidney
40	chr19:57036200-57037800	ZNF genes & repeats	Primary T cells from cord blood	blood
41	chr19:57036200-57038200	ZNF genes & repeats	HSMMtube	muscle
42	chr19:57036200-57038600	ZNF genes & repeats	Colonic Mucosa	Colon
43	chr19:57036400-57037800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
44	chr19:57036400-57038200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
45	chr19:57036400-57038400	ZNF genes & repeats	Aorta	Aorta
46	chr19:57036800-57037200	ZNF genes & repeats	A549	lung
47	chr19:57037000-57038400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin

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