Variant report

Variant	rs12462723
Chromosome Location	chr19:44769974-44769975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44764453..44767160-chr19:44768719..44770239,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10405450	0.81[EUR][1000 genomes]
rs10410086	0.81[EUR][1000 genomes]
rs10423306	0.82[EUR][1000 genomes]
rs10425945	0.85[CEU][hapmap]
rs10775542	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666199	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11667521	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11671074	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12459795	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12460431	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12461251	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12462557	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12609635	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs12972784	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12975315	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12975546	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12980565	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2014501	0.87[EUR][1000 genomes]
rs2051058	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2051059	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2085516	0.85[GIH][hapmap]
rs2100643	0.82[GIH][hapmap]
rs2125578	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2125579	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2168989	0.85[CEU][hapmap];0.92[GIH][hapmap];0.86[TSI][hapmap]
rs2232801	0.85[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap]
rs2279072	0.89[CEU][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs2279073	0.81[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2293587	0.85[GIH][hapmap]
rs2356727	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2356751	0.83[GIH][hapmap]
rs3817595	0.85[GIH][hapmap]
rs4592768	0.88[AMR][1000 genomes]
rs4802210	0.85[GIH][hapmap];0.91[JPT][hapmap]
rs4802217	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4802218	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803694	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509145	0.91[JPT][hapmap]
rs6509146	0.85[GIH][hapmap]
rs6509150	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249209	0.83[GIH][hapmap]
rs7251134	0.83[MEX][hapmap]
rs7251682	0.89[CEU][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs7252577	0.87[EUR][1000 genomes]
rs7253196	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7253533	0.85[CEU][hapmap]
rs7259916	0.81[EUR][1000 genomes]
rs7260304	0.89[CEU][hapmap];0.92[GIH][hapmap];0.86[TSI][hapmap]
rs7508523	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs8101032	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8102037	0.82[EUR][1000 genomes]
rs8103838	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs8105073	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8105479	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes]
rs8106766	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8108934	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8109462	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8109706	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9304640	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs9646642	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9646643	0.81[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521923	chr19:44764064-44769974	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12462723	ZNF528	cis	parietal	SCAN
rs12462723	RUVBL2	cis	parietal	SCAN
rs12462723	AKT1S1	cis	cerebellum	SCAN
rs12462723	ZNF233	cis	multi-tissue	Pritchard

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44730000-44775600	ZNF genes & repeats	Liver	Liver
2	chr19:44764600-44770000	Weak transcription	Fetal Kidney	kidney
3	chr19:44764600-44771000	Weak transcription	Psoas Muscle	Psoas
4	chr19:44764600-44778200	Weak transcription	HSMMtube	muscle
5	chr19:44764800-44770000	Weak transcription	Primary B cells from cord blood	blood
6	chr19:44764800-44770000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr19:44764800-44771200	Weak transcription	Thymus	Thymus
8	chr19:44764800-44777600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr19:44764800-44777600	Weak transcription	Placenta	Placenta
10	chr19:44764800-44782000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:44765000-44770000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:44765000-44770000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr19:44765000-44770200	Weak transcription	Fetal Intestine Small	intestine
14	chr19:44765000-44770200	Weak transcription	Fetal Stomach	stomach
15	chr19:44765000-44770200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr19:44765000-44770400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr19:44765000-44770400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr19:44765000-44770800	Weak transcription	Fetal Muscle Leg	muscle
19	chr19:44765000-44771000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr19:44765000-44771200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr19:44765000-44772400	Weak transcription	A549	lung
22	chr19:44765000-44772600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:44765000-44773400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr19:44765000-44774800	Weak transcription	Fetal Lung	lung
25	chr19:44765000-44774800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr19:44765000-44775400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr19:44765000-44777400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr19:44765000-44777400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr19:44765000-44777400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr19:44765000-44777400	Weak transcription	Fetal Heart	heart
31	chr19:44765000-44777600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr19:44765000-44777600	Weak transcription	Right Ventricle	heart
33	chr19:44765000-44778000	Weak transcription	Fetal Brain Male	brain
34	chr19:44765200-44770000	Weak transcription	Fetal Brain Female	brain
35	chr19:44765200-44777000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr19:44765200-44777600	Weak transcription	Dnd41	blood
37	chr19:44765400-44770000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr19:44765400-44770200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:44765400-44770200	Weak transcription	Left Ventricle	heart
40	chr19:44765400-44771000	Weak transcription	Brain Anterior Caudate	brain
41	chr19:44765400-44771400	Weak transcription	Fetal Intestine Large	intestine
42	chr19:44765400-44773600	Weak transcription	HepG2	liver
43	chr19:44765400-44777600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:44767200-44770200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr19:44767200-44770200	Weak transcription	Ovary	ovary
46	chr19:44767600-44777400	Weak transcription	Brain Angular Gyrus	brain
47	chr19:44767800-44770200	Weak transcription	Brain Substantia Nigra	brain
48	chr19:44768400-44770200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr19:44769200-44773200	Strong transcription	Brain Germinal Matrix	brain
50	chr19:44769400-44770200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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