Variant report

Variant	rs6445790
Chromosome Location	chr3:56470028-56470029
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1388255	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1491163	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1552668	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1552669	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1878269	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35139577	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4527348	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974214	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58145335	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6445792	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6762660	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6783666	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6784781	0.95[CEU][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6785094	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6796830	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6807444	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs725089	0.95[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7628279	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7637479	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7644198	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7646515	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812701	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9829542	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9856358	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9871408	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	esv3383044	chr3:56466497-56483664	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv3347557	chr3:56466500-56619322	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56456400-56479600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:56457600-56473400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:56458000-56474800	Weak transcription	Fetal Heart	heart
4	chr3:56466400-56471600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:56467200-56473000	Weak transcription	HUVEC	blood vessel
6	chr3:56467600-56470400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:56467600-56470600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:56468800-56470400	Weak transcription	Brain Germinal Matrix	brain
9	chr3:56468800-56471200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:56469000-56470400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:56469000-56470400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:56469000-56470600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:56469000-56471200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:56469000-56471200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:56469000-56471800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr3:56469000-56471800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:56469000-56472000	Weak transcription	Fetal Brain Female	brain
18	chr3:56469000-56479400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:56469000-56481000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:56469000-56492600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:56469600-56470200	Enhancers	HUES48 Cell Line	embryonic stem cell

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