Variant report

Variant	rs3929899
Chromosome Location	chr1:56795419-56795420
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10493203	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10493204	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11206790	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12731002	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12734287	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12739422	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12756361	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12759658	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17113726	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17113749	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17113759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3005914	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34290061	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34349805	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34897038	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34980788	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35476561	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6588618	1.00[AMR][1000 genomes]
rs71639717	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71639718	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71639720	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71639721	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71639722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7365902	0.94[ASN][1000 genomes]
rs7525535	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9786996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9787125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9787375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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	nsv1006422	chr1:56734772-56828606	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv534972	chr1:56734772-56828606	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv1015037	chr1:56784322-56814739	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56782000-56797000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:56787000-56805600	Weak transcription	Left Ventricle	heart
3	chr1:56787200-56800600	Weak transcription	Fetal Muscle Leg	muscle
4	chr1:56788400-56796200	Weak transcription	Psoas Muscle	Psoas
5	chr1:56791200-56820800	Weak transcription	Aorta	Aorta
6	chr1:56791800-56796000	Weak transcription	NH-A	brain
7	chr1:56792000-56795800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:56792200-56796000	Weak transcription	HUVEC	blood vessel
9	chr1:56792200-56797000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:56792400-56798200	Weak transcription	Ovary	ovary
11	chr1:56793200-56796600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:56793800-56797000	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr1:56794200-56797200	Enhancers	NHLF	lung
14	chr1:56794200-56798000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:56794200-56798200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:56794200-56798200	Enhancers	NHDF-Ad	bronchial
17	chr1:56794400-56796400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr1:56794400-56796600	Enhancers	HepG2	liver
19	chr1:56794400-56797200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:56794400-56797400	Enhancers	Osteobl	bone
21	chr1:56794400-56797800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:56794600-56796400	Enhancers	HSMMtube	muscle
23	chr1:56794600-56798000	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr1:56794600-56798000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:56794600-56798000	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr1:56794800-56795600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:56794800-56797000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:56794800-56797200	Enhancers	Placenta	Placenta
29	chr1:56795000-56796000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:56795000-56796000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:56795000-56797000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:56795200-56797000	Enhancers	GM12878-XiMat	blood
33	chr1:56795400-56795600	Enhancers	Fetal Heart	heart
34	chr1:56795400-56796400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:56795400-56796400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr1:56795400-56797000	Enhancers	Liver	Liver
37	chr1:56795400-56797000	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr1:56795400-56797400	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr1:56795400-56797800	Enhancers	Hela-S3	cervix
40	chr1:56795400-56798000	Enhancers	Placenta Amnion	Placenta Amnion
41	chr1:56795400-56798400	Enhancers	Fetal Intestine Small	intestine

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