Variant report

Variant	rs9973828
Chromosome Location	chr3:17742578-17742579
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11682910	0.81[ASN][1000 genomes]
rs11682979	0.82[ASN][1000 genomes]
rs11683030	0.87[ASN][1000 genomes]
rs11684334	0.89[ASN][1000 genomes]
rs11694147	0.82[ASN][1000 genomes]
rs11694212	0.82[ASN][1000 genomes]
rs12465480	0.90[ASN][1000 genomes]
rs12466554	0.87[ASN][1000 genomes]
rs12469765	0.90[EUR][1000 genomes]
rs12473646	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12474621	0.87[ASN][1000 genomes]
rs12477568	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12478416	0.88[ASN][1000 genomes]
rs12615919	0.89[ASN][1000 genomes]
rs13023587	0.83[EUR][1000 genomes]
rs13025387	0.85[ASN][1000 genomes]
rs13030816	0.88[ASN][1000 genomes]
rs1394201	0.86[EUR][1000 genomes]
rs2174278	0.83[EUR][1000 genomes]
rs34882825	0.82[ASN][1000 genomes]
rs35716340	0.86[ASN][1000 genomes]
rs4078370	0.80[ASN][1000 genomes]
rs4330135	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4337506	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4971701	0.81[ASN][1000 genomes]
rs4971702	0.81[ASN][1000 genomes]
rs4971715	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4971718	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4971728	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4971729	0.87[ASN][1000 genomes]
rs6419619	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6545101	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6753537	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7560929	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7575144	0.87[ASN][1000 genomes]
rs7575146	0.86[ASN][1000 genomes]
rs7578571	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7588963	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7598097	0.85[ASN][1000 genomes]
rs9712256	0.88[ASN][1000 genomes]
rs972557	0.84[EUR][1000 genomes]
rs9973500	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9973827	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013069	chr3:17560456-17783372	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv1849856	chr3:17646794-17748688	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv1828838	chr3:17646794-17757960	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv999594	chr3:17690416-17982318	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17711400-17755000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr3:17720000-17747400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:17731600-17755600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:17732200-17749400	Weak transcription	NHEK	skin
5	chr3:17732600-17755400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:17733200-17755600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:17733400-17747000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:17734800-17753200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:17735200-17747600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:17735200-17755600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:17735200-17755800	Weak transcription	Lung	lung
12	chr3:17735400-17750800	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr3:17735400-17754200	Weak transcription	Primary B cells from cord blood	blood
14	chr3:17735400-17755400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:17735400-17755600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:17735400-17755800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:17736000-17745000	Weak transcription	HepG2	liver
18	chr3:17736000-17747600	Weak transcription	Dnd41	blood

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