Variant report

Variant	rs7539738
Chromosome Location	chr1:85884024-85884025
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1001604	0.80[AFR][1000 genomes]
rs1006988	0.84[AMR][1000 genomes]
rs1006989	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10489510	0.81[EUR][1000 genomes]
rs10747318	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10782549	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10873701	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10873702	0.87[AFR][1000 genomes]
rs11161611	0.86[AFR][1000 genomes]
rs1146383	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12029221	0.87[EUR][1000 genomes]
rs12033483	0.89[EUR][1000 genomes]
rs12034249	0.89[EUR][1000 genomes]
rs12035116	0.83[EUR][1000 genomes]
rs12038426	0.83[EUR][1000 genomes]
rs12042780	0.81[EUR][1000 genomes]
rs12047189	0.81[EUR][1000 genomes]
rs1261681	0.85[EUR][1000 genomes]
rs1342323	0.89[EUR][1000 genomes]
rs1357635	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1357636	0.89[EUR][1000 genomes]
rs1391556	0.85[EUR][1000 genomes]
rs1523995	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1554597	0.86[AFR][1000 genomes]
rs1608537	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs17384213	0.89[EUR][1000 genomes]
rs17388696	0.87[EUR][1000 genomes]
rs1965876	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1975755	0.81[AFR][1000 genomes]
rs2011825	0.83[AFR][1000 genomes]
rs2016104	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2037594	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064510	0.85[EUR][1000 genomes]
rs2124139	0.89[EUR][1000 genomes]
rs2177461	0.83[AFR][1000 genomes]
rs2207368	0.83[AFR][1000 genomes]
rs2300633	0.83[EUR][1000 genomes]
rs2389948	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2840319	0.81[AFR][1000 genomes]
rs3851268	0.87[EUR][1000 genomes]
rs3949301	0.83[AFR][1000 genomes]
rs4428939	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4512701	0.85[EUR][1000 genomes]
rs4631749	0.85[EUR][1000 genomes]
rs4949889	0.82[EUR][1000 genomes]
rs4949897	0.82[EUR][1000 genomes]
rs4949898	0.83[EUR][1000 genomes]
rs4949899	0.85[EUR][1000 genomes]
rs499869	0.87[EUR][1000 genomes]
rs539714	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs600098	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs604974	0.87[EUR][1000 genomes]
rs6420965	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6576767	0.85[AFR][1000 genomes]
rs6657817	0.86[AFR][1000 genomes]
rs6671599	0.87[AFR][1000 genomes]
rs6672870	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6704103	0.86[AFR][1000 genomes]
rs67611930	0.83[AFR][1000 genomes]
rs72722663	0.82[EUR][1000 genomes]
rs72722691	0.83[EUR][1000 genomes]
rs72724606	0.82[AFR][1000 genomes]
rs72724608	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs731194	0.83[EUR][1000 genomes]
rs7515261	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7546931	0.86[AFR][1000 genomes]
rs7547571	0.81[AFR][1000 genomes]
rs7555670	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990916	0.89[EUR][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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1008877	chr1:85843238-85897570	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr1:85873600-85885000	Weak transcription	Fetal Intestine Large	intestine
2	chr1:85873800-85885400	Weak transcription	Fetal Stomach	stomach
3	chr1:85873800-85887600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:85874000-85903800	Weak transcription	NHLF	lung
5	chr1:85874200-85903600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:85874400-85903600	Weak transcription	HepG2	liver
7	chr1:85874400-85904200	Weak transcription	NH-A	brain
8	chr1:85875400-85885600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:85877200-85885600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:85877600-85885800	Weak transcription	HSMMtube	muscle
11	chr1:85879200-85885600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:85880400-85884400	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:85880400-85884400	Weak transcription	NHDF-Ad	bronchial
14	chr1:85880400-85887600	Weak transcription	Osteobl	bone
15	chr1:85880600-85884600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:85882400-85885000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:85883000-85885000	Weak transcription	Fetal Intestine Small	intestine
18	chr1:85883200-85884200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:85883200-85884200	Weak transcription	Ovary	ovary
20	chr1:85883200-85884400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:85883200-85885400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:85883200-85885600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:85883200-85887000	Weak transcription	HSMM	muscle
24	chr1:85883200-85893400	Weak transcription	Aorta	Aorta
25	chr1:85883800-85884400	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr1:85884000-85884400	Flanking Active TSS	HUVEC	blood vessel

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