Variant report

Variant	rs12972978
Chromosome Location	chr19:39517961-39517962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10406222	0.88[ASN][1000 genomes]
rs10416823	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10417436	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10424632	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10424827	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10426645	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10426661	0.86[ASN][1000 genomes]
rs1062261	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10853723	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10853724	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11083499	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11083500	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11083501	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11083502	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1139251	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11667641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670486	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11670520	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11673044	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11673637	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11880441	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11883422	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12609806	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12610200	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12610248	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12971842	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12972850	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12978163	0.92[ASN][1000 genomes]
rs12978749	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12982199	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12982349	0.94[ASN][1000 genomes]
rs12982529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12985447	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1651748	0.84[EUR][1000 genomes]
rs1840745	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1840746	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1840747	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1840748	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1864191	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1869983	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36154890	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3848623	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4280369	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802007	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802009	0.89[ASN][1000 genomes]
rs4803181	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803185	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803186	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803187	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803188	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803193	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58897626	0.87[ASN][1000 genomes]
rs60775146	0.87[ASN][1000 genomes]
rs62119538	0.88[ASN][1000 genomes]
rs628335	0.85[ASN][1000 genomes]
rs6508835	0.91[ASN][1000 genomes]
rs6508836	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6508837	0.91[ASN][1000 genomes]
rs6508838	0.94[ASN][1000 genomes]
rs6508839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6508840	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6508841	0.94[ASN][1000 genomes]
rs6508842	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6508843	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs681496	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7247801	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7248513	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7248652	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7250110	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7250431	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7251264	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7255211	0.95[ASN][1000 genomes]
rs7256126	0.93[ASN][1000 genomes]
rs7258862	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7259064	0.86[ASN][1000 genomes]
rs7259197	0.86[ASN][1000 genomes]
rs7259473	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7259801	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8100503	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8103187	0.90[ASN][1000 genomes]
rs8104751	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8104899	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8104990	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8105865	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109176	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12972978	CTB-189B5.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12972978	FBXO27	cis	Skin Sun Exposed Lower leg	GTEx
rs12972978	CTB-189B5.3	cis	Esophagus Mucosa	GTEx
rs12972978	FBXO27	cis	Esophagus Mucosa	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39487200-39518200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr19:39502400-39518000	Weak transcription	Aorta	Aorta
3	chr19:39503600-39520200	Weak transcription	Liver	Liver
4	chr19:39512400-39518000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr19:39513000-39521600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr19:39513000-39521600	Weak transcription	Right Atrium	heart
7	chr19:39514000-39521400	Weak transcription	Pancreas	Pancrea
8	chr19:39514000-39522200	Weak transcription	Gastric	stomach
9	chr19:39514400-39520400	Weak transcription	Fetal Intestine Large	intestine
10	chr19:39514400-39521600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr19:39514400-39521800	Weak transcription	Colon Smooth Muscle	Colon
12	chr19:39514600-39521400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:39514800-39518600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr19:39514800-39519600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:39514800-39520000	Strong transcription	Brain Cingulate Gyrus	brain
16	chr19:39515000-39518000	Strong transcription	Stomach Smooth Muscle	stomach
17	chr19:39515200-39521600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr19:39515400-39519000	Strong transcription	Brain Hippocampus Middle	brain
19	chr19:39515600-39518400	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr19:39515600-39518600	Strong transcription	Brain Substantia Nigra	brain
21	chr19:39515600-39518800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:39515800-39518000	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr19:39515800-39518400	Strong transcription	Adipose Nuclei	Adipose
24	chr19:39515800-39518600	Strong transcription	Ovary	ovary
25	chr19:39516000-39518200	Strong transcription	Brain Angular Gyrus	brain
26	chr19:39516200-39521000	Weak transcription	K562	blood
27	chr19:39516200-39521600	Weak transcription	Right Ventricle	heart
28	chr19:39516400-39518000	Weak transcription	Fetal Heart	heart
29	chr19:39516400-39522200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr19:39516600-39518400	ZNF genes & repeats	A549	lung
31	chr19:39516600-39518600	Strong transcription	Brain Anterior Caudate	brain
32	chr19:39516800-39518400	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr19:39516800-39518600	ZNF genes & repeats	Fetal Intestine Small	intestine
34	chr19:39517000-39518000	Weak transcription	Esophagus	oesophagus
35	chr19:39517400-39518000	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr19:39517400-39518000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr19:39517400-39518000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:39517400-39518400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr19:39517400-39518400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:39517400-39518400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr19:39517400-39518600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
42	chr19:39517400-39518600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr19:39517600-39518200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
44	chr19:39517600-39518200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr19:39517600-39518200	ZNF genes & repeats	Lung	lung
46	chr19:39517600-39518200	Enhancers	HepG2	liver
47	chr19:39517600-39518200	ZNF genes & repeats	NHEK	skin
48	chr19:39517600-39518400	Strong transcription	Pancreatic Islets	Pancreatic Islet
49	chr19:39517600-39518600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:39517600-39518600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell

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