Variant report

Variant	rs10399899
Chromosome Location	chr1:56432215-56432216
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10789013	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10789014	0.85[EUR][1000 genomes]
rs11206691	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11206698	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12079802	0.85[EUR][1000 genomes]
rs3862239	0.85[EUR][1000 genomes]
rs4927286	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658481	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6685644	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6685665	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7532348	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540718	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9436529	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870513	chr1:56407227-56493106	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1003385	chr1:56430742-56468732	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56425800-56441000	Weak transcription	Fetal Muscle Leg	muscle
2	chr1:56426800-56432800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:56427200-56434000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:56430400-56433800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:56431000-56432600	Enhancers	Placenta Amnion	Placenta Amnion
6	chr1:56431400-56432400	Enhancers	NHEK	skin
7	chr1:56431600-56432400	Enhancers	Primary hematopoietic stem cells	blood
8	chr1:56431600-56432400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:56431800-56432400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:56432000-56435800	Weak transcription	NHDF-Ad	bronchial
11	chr1:56432200-56432400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:56432200-56432400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:56432200-56435800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:56432200-56439800	Weak transcription	Osteobl	bone

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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