Variant report

Variant	rs929209
Chromosome Location	chr16:31743663-31743664
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1045483	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1073513	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1104549	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1104550	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11150632	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11150639	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11642525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11643629	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12325485	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12386038	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12921028	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]
rs12932938	0.85[AMR][1000 genomes];0.90[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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1358485	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1406177	0.82[CEU][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap]
rs1406178	1.00[CEU][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1468158	1.00[CEU][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1468159	1.00[CEU][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1528317	0.88[ASW][hapmap];1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1534506	0.83[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];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1609289	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1852667	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1881316	0.82[CEU][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap]
rs1881317	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1881318	0.88[ASW][hapmap];1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1919039	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2008774	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2078923	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2091521	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2097683	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2106580	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2141349	0.95[CEU][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2157969	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2188620	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2214139	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2359220	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2359223	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2359228	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2359231	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3088127	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34632985	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3751738	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3751742	1.00[CEU][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3937426	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4297693	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4499253	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4572414	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889679	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4889680	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4889687	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6565266	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6565270	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6565271	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6565277	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6565284	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7187074	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7188748	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7192274	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7192670	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7195700	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7197470	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7197963	1.00[CEU][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7198038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7498390	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8043927	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8048027	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[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];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8052434	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8054649	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9928006	0.83[MEX][hapmap]
rs9928595	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9929259	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9939255	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[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	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	nsv833195	chr16:31576112-31763222	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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
13	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
rs929209	ATP2A1	cis	cerebellum	SCAN
rs929209	ZNF720	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31725800-31753400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:31726000-31747400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr16:31726200-31745600	Weak transcription	Colonic Mucosa	Colon
4	chr16:31726400-31750000	Weak transcription	HUVEC	blood vessel
5	chr16:31726400-31750800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr16:31726600-31744000	Weak transcription	K562	blood
7	chr16:31726600-31748600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr16:31727000-31745000	Weak transcription	HMEC	breast
9	chr16:31727200-31758800	Weak transcription	Fetal Thymus	thymus
10	chr16:31727200-31760000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr16:31727600-31758400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr16:31727800-31744800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr16:31727800-31748400	Weak transcription	HSMMtube	muscle
14	chr16:31728000-31752200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr16:31730000-31758200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr16:31730200-31751000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr16:31731600-31748200	Weak transcription	Right Ventricle	heart
18	chr16:31733600-31743800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
19	chr16:31735000-31748200	Weak transcription	Osteobl	bone
20	chr16:31735200-31751000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr16:31738800-31745600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr16:31738800-31758200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr16:31739000-31754600	ZNF genes & repeats	Liver	Liver
24	chr16:31739400-31743800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
25	chr16:31740400-31743800	ZNF genes & repeats	GM12878-XiMat	blood
26	chr16:31740400-31744000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr16:31740600-31743800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
28	chr16:31740600-31744000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr16:31740800-31745200	Weak transcription	NHDF-Ad	bronchial
30	chr16:31740800-31751000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr16:31741400-31743800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
32	chr16:31741600-31744600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr16:31741800-31743800	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr16:31742000-31744000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
35	chr16:31742200-31744200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr16:31742400-31744000	Strong transcription	Fetal Intestine Large	intestine
37	chr16:31742400-31744000	Strong transcription	HSMM	muscle
38	chr16:31742800-31744600	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr16:31742800-31744800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr16:31742800-31745000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr16:31742800-31745400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr16:31742800-31745400	Weak transcription	Dnd41	blood
43	chr16:31742800-31745600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr16:31742800-31746000	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr16:31742800-31746600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr16:31742800-31746600	Weak transcription	Brain Germinal Matrix	brain
47	chr16:31742800-31746800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr16:31742800-31747000	Weak transcription	Placenta	Placenta
49	chr16:31742800-31747200	Weak transcription	Brain Anterior Caudate	brain
50	chr16:31742800-31749400	Weak transcription	Psoas Muscle	Psoas

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