Variant report

Variant	rs1938299
Chromosome Location	chr1:45744810-45744811
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1502340	1.00[AFR][1000 genomes]
rs17394390	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs17397799	1.00[AFR][1000 genomes]
rs2096435	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4660298	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4660299	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4660837	1.00[AFR][1000 genomes]
rs4660838	1.00[CEU][hapmap]
rs4660840	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes]
rs58612171	0.92[EUR][1000 genomes]
rs61788378	1.00[AFR][1000 genomes]
rs61788379	1.00[AFR][1000 genomes]
rs61788380	1.00[AFR][1000 genomes]
rs61788382	1.00[AFR][1000 genomes]
rs61788388	1.00[AFR][1000 genomes]
rs61788389	1.00[AFR][1000 genomes]
rs61788390	1.00[AFR][1000 genomes]
rs61788393	1.00[AFR][1000 genomes]
rs61788428	1.00[AFR][1000 genomes]
rs61788429	1.00[AFR][1000 genomes]
rs61788430	1.00[AFR][1000 genomes]
rs61788436	1.00[AFR][1000 genomes]
rs61788438	1.00[AFR][1000 genomes]
rs61788439	1.00[AFR][1000 genomes]
rs61788440	1.00[AFR][1000 genomes]
rs61788441	1.00[AFR][1000 genomes]
rs61788447	1.00[AFR][1000 genomes]
rs61788449	1.00[AFR][1000 genomes]
rs61788455	1.00[AFR][1000 genomes]
rs61789766	1.00[AFR][1000 genomes]
rs61789768	1.00[AFR][1000 genomes]
rs61789773	0.84[EUR][1000 genomes]
rs61789774	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs61789775	1.00[AFR][1000 genomes]
rs61789777	1.00[AFR][1000 genomes]
rs61789778	1.00[AFR][1000 genomes]
rs61789782	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs61789785	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61789788	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61789789	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61789808	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61789809	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61789814	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61789816	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61789817	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61789818	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61789819	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61789820	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61789821	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61789822	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61789826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61789830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
4	nsv1014509	chr1:45687523-45887501	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	esv3406025	chr1:45739908-45763848	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1938299	UTS2	trans	lymphoblastoid	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45732400-45748000	Weak transcription	Right Atrium	heart
2	chr1:45741000-45750800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:45741800-45749000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links