Variant report

Variant	rs12092295
Chromosome Location	chr1:227836291-227836292
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	chr1:227831322..227834251-chr1:227834809..227836572,2	K562	blood:

Variant related genes	Relation type
ENSG00000265216	Chromatin interaction
ENSG00000181450	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10047205	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916178	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916192	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12059899	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12069550	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12070539	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12080590	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12082414	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12095502	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12096675	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1495846	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1495849	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16847966	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16847991	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16847992	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16848029	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1923821	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2012432	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2132366	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2256599	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2453682	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2644143	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2644144	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2644146	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2644153	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2644161	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2814059	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2814060	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2814061	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2814084	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2814085	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2819496	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2819498	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2819507	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2819511	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3748806	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4376731	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4589104	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58020705	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59034043	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59149651	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59753688	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61343450	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66471275	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66491073	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6659745	0.84[EUR][1000 genomes]
rs66736638	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6688145	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6693348	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66938123	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67216605	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67511833	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67676707	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68046179	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68186506	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72632830	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72632831	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72632832	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72748074	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7413796	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs753541	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7539151	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs903692	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs903693	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs903694	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs903695	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs965942	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12092295	C1orf142	Cis_1M	lymphoblastoid	RTeQTL
rs12092295	ZNF678	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 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	chr1:227819800-227837600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:227820600-227861600	ZNF genes & repeats	Adipose Nuclei	Adipose
4	chr1:227827800-227845400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
5	chr1:227828400-227837400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
6	chr1:227829400-227859800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:227829600-227837600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
8	chr1:227830800-227845200	ZNF genes & repeats	Dnd41	blood
9	chr1:227831600-227837400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
10	chr1:227831800-227837400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:227831800-227837400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
12	chr1:227831800-227837600	ZNF genes & repeats	Primary T cells from cord blood	blood
13	chr1:227831800-227839800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
14	chr1:227831800-227840000	ZNF genes & repeats	Primary B cells from cord blood	blood
15	chr1:227831800-227850200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
16	chr1:227831800-227851600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:227831800-227854600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
18	chr1:227831800-227864000	ZNF genes & repeats	Liver	Liver
19	chr1:227832000-227837400	ZNF genes & repeats	Fetal Lung	lung
20	chr1:227832000-227843600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
21	chr1:227832000-227845200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
22	chr1:227832000-227850200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
23	chr1:227832000-227854400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
24	chr1:227832200-227837400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:227832200-227850600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:227832400-227837600	ZNF genes & repeats	Brain Hippocampus Middle	brain
27	chr1:227832400-227850400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
28	chr1:227832600-227846400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
29	chr1:227833400-227849600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
30	chr1:227833600-227837200	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
31	chr1:227833800-227837600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:227833800-227838800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:227834000-227836800	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:227834000-227837000	ZNF genes & repeats	A549	lung
35	chr1:227834000-227837200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:227834000-227837400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:227834000-227838000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr1:227834000-227839600	ZNF genes & repeats	Brain Anterior Caudate	brain
39	chr1:227834000-227843800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
40	chr1:227834000-227847200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:227834200-227837400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
42	chr1:227834200-227837600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:227834400-227837600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:227834400-227838800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:227834600-227836600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:227834600-227837400	ZNF genes & repeats	Ovary	ovary
47	chr1:227834800-227838000	ZNF genes & repeats	Fetal Intestine Large	intestine
48	chr1:227835000-227836600	ZNF genes & repeats	Fetal Muscle Leg	muscle
49	chr1:227835000-227836600	ZNF genes & repeats	Right Ventricle	heart
50	chr1:227835000-227852200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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