Variant report

Variant	rs1339592
Chromosome Location	chr1:192937900-192937901
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1339589	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1578163	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1612628	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1618583	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1769055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1769056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1769057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1769058	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1769059	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1769061	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1769068	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1769070	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1769071	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1770923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2486494	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2486495	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2486498	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2487283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2487289	0.97[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59189492	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6661948	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73068182	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73068192	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7546076	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7553594	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs842784	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842787	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842788	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842789	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842799	0.97[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842800	0.97[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842801	0.97[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842805	0.89[YRI][hapmap]
rs842806	0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842807	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842808	0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842809	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842810	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842811	0.97[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842813	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs863600	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs866380	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs866381	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs946556	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532618	chr1:192537006-193149179	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv548660	chr1:192609268-192945348	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv999499	chr1:192909529-192998421	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv535252	chr1:192909529-192998421	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:192922400-192941000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:192936400-192938400	Enhancers	K562	blood
3	chr1:192936400-192939000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:192936600-192938200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:192936600-192938200	Enhancers	Duodenum Mucosa	Duodenum
6	chr1:192936600-192938800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:192936600-192938800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr1:192936600-192939200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:192936600-192939200	Enhancers	Osteobl	bone
10	chr1:192936800-192938000	Enhancers	Fetal Intestine Large	intestine
11	chr1:192936800-192938000	Enhancers	Hela-S3	cervix
12	chr1:192936800-192938400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:192936800-192938400	Enhancers	HSMM	muscle
14	chr1:192936800-192939200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:192936800-192939200	Enhancers	Muscle Satellite Cultured Cells	--
16	chr1:192937000-192938400	Enhancers	HUVEC	blood vessel
17	chr1:192937000-192963400	Weak transcription	Aorta	Aorta
18	chr1:192937200-192938200	Enhancers	Fetal Intestine Small	intestine
19	chr1:192937400-192939800	Weak transcription	Stomach Mucosa	stomach
20	chr1:192937600-192938200	Enhancers	HepG2	liver
21	chr1:192937800-192938000	Enhancers	Pancreas	Pancrea
22	chr1:192937800-192938000	Enhancers	Psoas Muscle	Psoas
23	chr1:192937800-192938000	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr1:192937800-192939800	Weak transcription	Small Intestine	intestine
25	chr1:192937800-192940400	Weak transcription	HSMMtube	muscle
26	chr1:192937800-192946600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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