Variant report

Variant	rs12142639
Chromosome Location	chr1:153846124-153846125
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153844859..153847252-chr1:153894099..153896023,2	K562	blood:
2	chr1:153792838..153795369-chr1:153845133..153846957,2	K562	blood:

Variant related genes	Relation type
ENSG00000143614	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10127484	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908512	0.87[EUR][1000 genomes]
rs10908525	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908526	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264573	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264621	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264736	0.86[ASN][1000 genomes]
rs1127091	0.80[EUR][1000 genomes]
rs1139620	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11800001	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120118	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12124424	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12130611	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12133492	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12142733	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12738361	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2252508	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35711150	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4276953	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4341393	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4370789	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4451582	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4540690	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4581307	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4596938	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61803655	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6427300	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6427306	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6661009	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6668066	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6671362	0.82[AMR][1000 genomes]
rs6677794	0.81[EUR][1000 genomes]
rs72694233	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7414227	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7415004	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7522030	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7549032	0.82[EUR][1000 genomes]
rs7554469	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9426935	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9426938	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9427232	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9427233	0.81[EUR][1000 genomes];0.86[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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv817392	chr1:153724807-153870005	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153800800-153850800	Weak transcription	A549	lung
2	chr1:153800800-153852800	Weak transcription	Fetal Brain Female	brain
3	chr1:153800800-153852800	Weak transcription	Placenta	Placenta
4	chr1:153800800-153852800	Weak transcription	Left Ventricle	heart
5	chr1:153800800-153853000	Weak transcription	Fetal Kidney	kidney
6	chr1:153814800-153848000	Weak transcription	Fetal Heart	heart
7	chr1:153814800-153853400	Weak transcription	HSMMtube	muscle
8	chr1:153822800-153853400	Weak transcription	HMEC	breast
9	chr1:153822800-153854200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:153825800-153852400	Weak transcription	Fetal Lung	lung
11	chr1:153825800-153853000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:153825800-153853000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:153825800-153853200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:153825800-153853200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:153825800-153887200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:153826000-153848000	Weak transcription	K562	blood
17	chr1:153826000-153853200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:153826000-153853400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:153826200-153852800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:153826200-153853200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:153828800-153852800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:153830200-153863600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:153831800-153853000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:153833400-153854400	Weak transcription	Gastric	stomach
25	chr1:153833600-153853600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:153836400-153847400	Weak transcription	Fetal Muscle Leg	muscle
27	chr1:153836800-153847600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:153836800-153849000	Weak transcription	HepG2	liver
29	chr1:153837000-153893000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:153837200-153853400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:153839200-153847400	Weak transcription	Dnd41	blood
32	chr1:153839200-153852200	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:153839200-153853000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:153839200-153853000	Weak transcription	Adipose Nuclei	Adipose
35	chr1:153839200-153853000	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:153839200-153853000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr1:153839200-153853400	Weak transcription	NHDF-Ad	bronchial
38	chr1:153839400-153848800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:153839600-153847400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:153839600-153848000	Weak transcription	Stomach Mucosa	stomach
41	chr1:153839800-153853000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:153839800-153853400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:153839800-153853400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr1:153840000-153853400	Weak transcription	Liver	Liver
45	chr1:153840200-153848800	Weak transcription	Primary T cells from cord blood	blood
46	chr1:153841400-153848800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:153842000-153850400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:153842200-153852000	Weak transcription	Brain Germinal Matrix	brain
49	chr1:153842200-153853600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:153842400-153847200	Weak transcription	Fetal Stomach	stomach

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