Variant report

Variant	rs12921028
Chromosome Location	chr16:31770723-31770724
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF720-3	chr16:31770678-31770787	NONHSAT141963
2	lnc-ZNF720-3	chr16:31770678-31770874	NONHSAT141962

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1045483	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1073513	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1104549	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1104550	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11150632	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11150639	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11642525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11643629	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12325485	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12386038	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12932938	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1304163	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1358485	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1406177	0.82[CEU][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap]
rs1406178	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1468158	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1468159	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1528317	0.88[ASW][hapmap];1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1534506	0.80[EUR][1000 genomes]
rs1599855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1609289	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1852667	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1881316	0.82[CEU][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap]
rs1881317	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1881318	0.88[ASW][hapmap];1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1919039	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2008774	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2078923	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2091521	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2097683	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2106580	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2141349	0.95[CEU][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2157969	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2188620	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2214139	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2359220	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2359223	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2359228	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2359231	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3088127	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34632985	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3751738	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3751742	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3937426	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4297693	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4499253	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4572414	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4632148	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4889679	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4889680	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4889687	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6565266	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6565270	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6565271	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6565277	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6565284	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7187074	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7188748	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7192274	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7192670	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7195700	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7197470	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7197963	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7198038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7359491	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7498390	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8043927	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8048027	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8048741	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8052434	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8054649	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs929209	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9928595	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9929259	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9939255	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv905747	chr16:31394179-31888684	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	123 gene(s)	inside rSNPs	diseases
2	esv3344221	chr16:31526786-31821640	Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	esv3323903	chr16:31526802-31821640	Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	esv3504445	chr16:31526873-31821580	Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	esv3504446	chr16:31526873-31821580	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	esv3366795	chr16:31534951-31827424	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
7	nsv1067321	chr16:31652036-31959992	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
8	nsv918074	chr16:31669781-31935033	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	nsv1063037	chr16:31669981-31934894	Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
10	nsv542903	chr16:31669981-31934894	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv905761	chr16:31730525-31812442	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv3446880	chr16:31734687-31891223	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12921028	ATP2A1	cis	cerebellum	SCAN
rs12921028	ZNF720	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31755400-31771000	ZNF genes & repeats	Liver	Liver
2	chr16:31756400-31771000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr16:31759600-31770800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr16:31759600-31771000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
5	chr16:31759600-31771000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
6	chr16:31759600-31771000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr16:31759600-31771000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr16:31759600-31771000	ZNF genes & repeats	Adipose Nuclei	Adipose
9	chr16:31759600-31771000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
10	chr16:31759800-31770800	ZNF genes & repeats	Brain Anterior Caudate	brain
11	chr16:31759800-31771000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
12	chr16:31759800-31771000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr16:31759800-31772600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
14	chr16:31759800-31788600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr16:31760200-31771000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
16	chr16:31762800-31771000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr16:31763200-31771000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr16:31763400-31771000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
19	chr16:31763600-31770800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
20	chr16:31763600-31771000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
21	chr16:31764000-31770800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr16:31764200-31771000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr16:31764200-31771000	ZNF genes & repeats	Fetal Brain Female	brain
24	chr16:31764200-31772200	Weak transcription	Pancreas	Pancrea
25	chr16:31766800-31774600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr16:31768800-31772200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr16:31768800-31775000	Weak transcription	Thymus	Thymus
28	chr16:31769000-31772200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr16:31769200-31773600	Weak transcription	Fetal Heart	heart
30	chr16:31769600-31770800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr16:31769600-31770800	ZNF genes & repeats	HSMMtube	muscle
32	chr16:31769600-31772000	Weak transcription	Brain Substantia Nigra	brain
33	chr16:31769600-31772200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr16:31769600-31772200	Weak transcription	NH-A	brain
35	chr16:31769800-31772200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr16:31770000-31772000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr16:31770000-31772000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr16:31770000-31772200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr16:31770000-31772200	Weak transcription	Ovary	ovary
40	chr16:31770200-31772000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr16:31770200-31772200	Weak transcription	Left Ventricle	heart
42	chr16:31770200-31773400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr16:31770400-31771000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr16:31770600-31770800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin

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