Variant report

Variant	rs1829308
Chromosome Location	chr1:223505111-223505112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223504054..223506980-chr1:223508583..223510799,2	K562	blood:
2	chr1:223502794..223505270-chr1:223535922..223537884,2	MCF-7	breast:
3	chr1:223503941..223506228-chr1:223511294..223513326,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143502	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1341289	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1518040	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1539047	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17163789	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17163816	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17163818	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1829309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1850562	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1856933	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1935037	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2096082	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2138970	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2176504	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2176505	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2176506	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34238669	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34468460	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35318812	0.83[AFR][1000 genomes]
rs4661238	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4661239	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61838234	0.85[AFR][1000 genomes]
rs61838235	0.85[AFR][1000 genomes]
rs61838236	0.83[AFR][1000 genomes]
rs61838237	0.83[AFR][1000 genomes]
rs61838241	0.84[AFR][1000 genomes]
rs66531524	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs66768536	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66867621	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67707169	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7536652	0.86[AFR][1000 genomes]
rs7541162	0.84[AFR][1000 genomes]
rs825127	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs825128	0.84[AFR][1000 genomes]
rs825131	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1000039	chr1:223429733-223527845	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1010798	chr1:223498145-223538989	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223497200-223512600	Weak transcription	Pancreas	Pancrea
2	chr1:223497400-223510400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:223501400-223506400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr1:223503000-223505600	Enhancers	Ovary	ovary
5	chr1:223503000-223506000	Weak transcription	Esophagus	oesophagus
6	chr1:223503800-223505800	Enhancers	Fetal Lung	lung
7	chr1:223504000-223505400	Enhancers	Aorta	Aorta
8	chr1:223504000-223506000	Enhancers	HMEC	breast
9	chr1:223504200-223505200	Weak transcription	Fetal Kidney	kidney
10	chr1:223504200-223505600	Enhancers	Primary T cells from cord blood	blood
11	chr1:223504200-223505600	Enhancers	Primary T cells fromperipheralblood	blood
12	chr1:223504200-223505600	Enhancers	Right Atrium	heart
13	chr1:223504200-223506600	Enhancers	Fetal Thymus	thymus
14	chr1:223504400-223505600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr1:223504400-223505600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr1:223504400-223506000	Enhancers	NHEK	skin
17	chr1:223504400-223506800	Enhancers	Fetal Heart	heart
18	chr1:223504400-223507000	Weak transcription	Brain Anterior Caudate	brain
19	chr1:223504600-223505400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:223504600-223505400	Bivalent Enhancer	Fetal Muscle Leg	muscle
21	chr1:223504600-223505600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:223504600-223505600	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr1:223504600-223505800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:223504800-223505400	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr1:223504800-223505600	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr1:223504800-223505600	Bivalent Enhancer	Osteobl	bone
27	chr1:223504800-223506200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:223504800-223506200	Enhancers	NH-A	brain
29	chr1:223505000-223505200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:223505000-223505400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:223505000-223505400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr1:223505000-223505600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:223505000-223505600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:223505000-223505600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:223505000-223505600	Enhancers	HSMM	muscle
36	chr1:223505000-223505600	Enhancers	HSMMtube	muscle
37	chr1:223505000-223505600	Enhancers	NHLF	lung
38	chr1:223505000-223505800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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