Variant report

Variant	rs11084454
Chromosome Location	chr19:57093168-57093169
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10405702	0.84[ASN][1000 genomes]
rs10406660	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10408033	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10409531	1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10410277	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10412249	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10413682	0.91[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10415256	0.85[ASN][1000 genomes]
rs10419789	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10421285	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10424437	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10425965	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10426619	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10427145	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1052280	0.86[ASN][1000 genomes]
rs12104204	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12104288	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12979383	0.98[ASN][1000 genomes]
rs12981572	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2024396	0.85[ASN][1000 genomes]
rs28428635	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28668141	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869896	0.82[ASN][1000 genomes]
rs2904241	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4401145	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4801174	0.86[ASN][1000 genomes]
rs4801335	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4801337	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4801339	0.86[ASN][1000 genomes]
rs4801343	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7252022	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7252934	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253371	1.00[CHB][hapmap];0.81[CHD][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.85[ASN][1000 genomes]
rs7253545	1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.85[ASN][1000 genomes]
rs7254001	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7258886	1.00[CHB][hapmap];0.83[CHD][hapmap];0.80[MEX][hapmap];0.86[ASN][1000 genomes]
rs7259161	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259577	0.86[ASN][1000 genomes]
rs7259608	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259741	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs741252	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs759331	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs764999	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs765000	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8101497	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8106879	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8108667	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9916995	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs995934	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11084454	ZFP28	cis	multi-tissue	Pritchard
rs11084454	ZNF776	cis	parietal	SCAN
rs11084454	ZFP28	cis	lymphoblastoid	seeQTL
rs11084454	ZSCAN22	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:57079200-57093400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:57079600-57094200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr19:57079600-57094400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
4	chr19:57079600-57095600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
5	chr19:57079800-57093600	ZNF genes & repeats	Primary T cells from cord blood	blood
6	chr19:57079800-57094400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:57079800-57094600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:57079800-57095400	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
9	chr19:57079800-57096000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr19:57079800-57096200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr19:57079800-57096200	ZNF genes & repeats	Adipose Nuclei	Adipose
12	chr19:57079800-57100000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
13	chr19:57079800-57101800	ZNF genes & repeats	Liver	Liver
14	chr19:57080000-57094600	ZNF genes & repeats	Brain Anterior Caudate	brain
15	chr19:57080000-57094800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:57080400-57094600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
17	chr19:57080800-57095200	ZNF genes & repeats	Fetal Brain Female	brain
18	chr19:57083800-57094800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
19	chr19:57084200-57093400	ZNF genes & repeats	Brain Germinal Matrix	brain
20	chr19:57084200-57094600	ZNF genes & repeats	Brain Substantia Nigra	brain
21	chr19:57084600-57094400	ZNF genes & repeats	Brain Cingulate Gyrus	brain
22	chr19:57087600-57094600	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:57087600-57095200	ZNF genes & repeats	Brain Hippocampus Middle	brain
24	chr19:57091600-57094600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
25	chr19:57092200-57093200	Weak transcription	Aorta	Aorta
26	chr19:57092200-57093200	Weak transcription	Left Ventricle	heart

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