Variant report

Variant	rs2967459
Chromosome Location	chr19:37092535-37092536
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1035777	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs10402182	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10403456	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10407919	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11084861	1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs11666769	0.83[ASN][1000 genomes]
rs11667894	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11668432	0.85[ASN][1000 genomes]
rs11668689	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11669816	0.90[ASN][1000 genomes]
rs11670914	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11671382	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11672098	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12608459	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12608512	0.87[ASN][1000 genomes]
rs12610555	0.85[ASN][1000 genomes]
rs12610572	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1357879	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1464830	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1464831	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1525133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1673082	0.81[ASN][1000 genomes]
rs17272386	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1985980	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2052728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2162296	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs2194976	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2912399	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2912400	0.89[ASN][1000 genomes]
rs2912404	0.85[ASN][1000 genomes]
rs2912408	0.92[ASN][1000 genomes]
rs2912412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2912440	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2912442	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2912443	0.94[ASN][1000 genomes]
rs2912444	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2912446	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2945964	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2945978	0.81[ASN][1000 genomes]
rs2967427	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2967429	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs2967436	0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.88[ASN][1000 genomes]
rs2967437	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2967438	0.92[ASN][1000 genomes]
rs2967439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967442	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967461	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2967463	0.90[ASN][1000 genomes]
rs2967464	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2967473	0.95[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs3096620	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3096637	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108593	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35299345	0.85[ASN][1000 genomes]
rs4806338	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4806339	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4806348	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4806349	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55940011	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55965207	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60213885	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60297398	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61457535	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61628442	0.83[ASN][1000 genomes]
rs6510551	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66717711	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66783290	0.90[ASN][1000 genomes]
rs67258954	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67995015	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68012004	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7246216	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7251805	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73609113	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7507224	1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs8100381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8108985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs826987	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised 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	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
7	esv3434386	chr19:37073454-37114509	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2967459	ZNF285	cis	parietal	SCAN
rs2967459	ZNF567	Cis_1M	lymphoblastoid	RTeQTL
rs2967459	PSG8	cis	cerebellum	SCAN
rs2967459	HNRNPUL1	cis	parietal	SCAN
rs2967459	SARS2	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37065600-37095400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:37070000-37095400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:37079800-37095200	Weak transcription	NH-A	brain
4	chr19:37080200-37095200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:37080400-37095000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr19:37080400-37095000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr19:37080400-37095000	Weak transcription	Fetal Muscle Leg	muscle
8	chr19:37080600-37094600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr19:37080600-37095200	Weak transcription	Right Ventricle	heart
10	chr19:37080600-37095200	Weak transcription	HSMMtube	muscle
11	chr19:37080800-37093800	Weak transcription	Fetal Brain Male	brain
12	chr19:37080800-37095000	Weak transcription	Brain Hippocampus Middle	brain
13	chr19:37080800-37095200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:37080800-37095200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr19:37080800-37095200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr19:37081000-37093800	Weak transcription	Dnd41	blood
17	chr19:37081200-37095000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr19:37081200-37095200	Weak transcription	Left Ventricle	heart
19	chr19:37082200-37095200	Weak transcription	Fetal Lung	lung
20	chr19:37083800-37094400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr19:37085400-37095000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:37085400-37095000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr19:37085600-37095000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr19:37085600-37095200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr19:37086400-37095000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr19:37087600-37095000	Weak transcription	Fetal Stomach	stomach
27	chr19:37087600-37095200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:37088000-37094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr19:37088600-37094200	Weak transcription	Primary T cells from cord blood	blood
30	chr19:37088600-37095200	Weak transcription	HSMM	muscle
31	chr19:37088600-37095400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr19:37089000-37094200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr19:37089400-37094600	Weak transcription	Brain Germinal Matrix	brain
34	chr19:37090000-37095400	Weak transcription	Esophagus	oesophagus
35	chr19:37090800-37095200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr19:37091200-37094400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr19:37091200-37095000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr19:37092000-37095000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr19:37092000-37095200	Weak transcription	Fetal Thymus	thymus
40	chr19:37092400-37095000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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