Variant report

Variant	rs3005912
Chromosome Location	chr1:56794997-56794998
allele	C/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]
rs12741124	0.86[EUR][1000 genomes]
rs2793659	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2994548	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2994549	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2994552	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2994554	0.80[AMR][1000 genomes]
rs2994555	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2994556	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2994557	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2994558	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2994565	0.88[EUR][1000 genomes]
rs3005883	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3005885	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3005886	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3005887	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3005892	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3005893	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3005894	0.80[AMR][1000 genomes]
rs3005895	0.80[AMR][1000 genomes]
rs3005897	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3005898	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3005899	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3005901	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3005909	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3005913	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6588617	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6670302	0.84[EUR][1000 genomes]
rs72916227	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56765200-56795400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:56782000-56797000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:56787000-56805600	Weak transcription	Left Ventricle	heart
4	chr1:56787200-56800600	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:56788400-56796200	Weak transcription	Psoas Muscle	Psoas
6	chr1:56791200-56820800	Weak transcription	Aorta	Aorta
7	chr1:56791800-56796000	Weak transcription	NH-A	brain
8	chr1:56792000-56795800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:56792200-56796000	Weak transcription	HUVEC	blood vessel
10	chr1:56792200-56797000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:56792400-56798200	Weak transcription	Ovary	ovary
12	chr1:56793200-56796600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:56793800-56795400	Weak transcription	Fetal Heart	heart
14	chr1:56793800-56797000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr1:56794000-56795400	Weak transcription	Liver	Liver
16	chr1:56794200-56795000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:56794200-56795000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr1:56794200-56797200	Enhancers	NHLF	lung
19	chr1:56794200-56798000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:56794200-56798200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:56794200-56798200	Enhancers	NHDF-Ad	bronchial
22	chr1:56794400-56796400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr1:56794400-56796600	Enhancers	HepG2	liver
24	chr1:56794400-56797200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:56794400-56797400	Enhancers	Osteobl	bone
26	chr1:56794400-56797800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:56794600-56795000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr1:56794600-56796400	Enhancers	HSMMtube	muscle
29	chr1:56794600-56798000	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr1:56794600-56798000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:56794600-56798000	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr1:56794800-56795000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:56794800-56795000	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr1:56794800-56795200	Weak transcription	GM12878-XiMat	blood
35	chr1:56794800-56795400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr1:56794800-56795600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:56794800-56797000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:56794800-56797200	Enhancers	Placenta	Placenta

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