Variant report

Variant	rs12069550
Chromosome Location	chr1:227800890-227800891
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10047205	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916178	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916192	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12059899	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12070539	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12080590	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12082414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12092295	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12095502	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12096675	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1495846	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1495849	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16847966	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16847991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16847992	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16848029	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1923821	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2012432	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2132366	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2256599	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2453682	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2644143	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2644144	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2644146	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2644153	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2644161	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2814059	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2814060	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2814061	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2814084	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2814085	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2819496	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2819498	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2819507	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2819511	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3748806	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4376731	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4589104	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58020705	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59034043	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59149651	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59753688	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61343450	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66471275	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66491073	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659745	0.87[EUR][1000 genomes]
rs66736638	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6688145	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693348	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66938123	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67216605	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67511833	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67676707	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68046179	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68186506	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72632830	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72632831	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72632832	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72748074	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7413796	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs753541	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7539151	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs903692	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs903693	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs903694	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs903695	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs965942	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	esv3327012	chr1:227741102-227890968	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv945673	chr1:227799341-227819395	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12069550	ZNF678	Cis_1M	lymphoblastoid	RTeQTL
rs12069550	C1orf142	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227770000-227853800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:227774800-227805000	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:227790400-227834800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:227790800-227801800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:227791400-227801000	Weak transcription	Psoas Muscle	Psoas
6	chr1:227794400-227804400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:227794600-227802000	Weak transcription	Placenta	Placenta
8	chr1:227794600-227808600	Weak transcription	Left Ventricle	heart
9	chr1:227795200-227801200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:227795200-227807000	Weak transcription	Fetal Heart	heart
11	chr1:227796200-227807200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:227796800-227801600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:227796800-227806000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:227797400-227803400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:227797600-227804800	ZNF genes & repeats	Fetal Stomach	stomach
16	chr1:227797800-227804800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr1:227797800-227805800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
18	chr1:227797800-227806400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
19	chr1:227797800-227807200	ZNF genes & repeats	Fetal Brain Female	brain
20	chr1:227798000-227804200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:227798000-227806400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
22	chr1:227798200-227801200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:227798200-227801400	ZNF genes & repeats	Primary B cells from cord blood	blood
24	chr1:227798200-227806800	ZNF genes & repeats	Brain Germinal Matrix	brain
25	chr1:227798200-227806800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
26	chr1:227798200-227806800	ZNF genes & repeats	Fetal Muscle Leg	muscle
27	chr1:227798200-227808000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:227798400-227801000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
29	chr1:227798400-227801000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
30	chr1:227798400-227801400	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:227798400-227802200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:227798600-227801400	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:227798600-227801800	ZNF genes & repeats	Fetal Intestine Small	intestine
34	chr1:227798600-227803400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:227798800-227802400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
36	chr1:227799000-227804000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
37	chr1:227799200-227801200	Strong transcription	Stomach Smooth Muscle	stomach
38	chr1:227799200-227801600	Strong transcription	Ovary	ovary
39	chr1:227799200-227802200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:227799400-227801000	Strong transcription	Primary T cells from cord blood	blood
41	chr1:227799400-227801200	ZNF genes & repeats	Aorta	Aorta
42	chr1:227799400-227805000	ZNF genes & repeats	Lung	lung
43	chr1:227799600-227801600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr1:227799800-227801600	Strong transcription	Fetal Intestine Large	intestine
45	chr1:227799800-227801800	Strong transcription	Primary B cells from peripheral blood	blood
46	chr1:227800000-227801000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:227800000-227801400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:227800000-227802600	Weak transcription	Brain Anterior Caudate	brain
49	chr1:227800000-227803600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr1:227800200-227802800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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