Variant report

Variant	rs293638
Chromosome Location	chr5:106067212-106067213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1036562	0.84[EUR][1000 genomes]
rs1036564	0.84[EUR][1000 genomes]
rs1036565	0.84[EUR][1000 genomes]
rs1036566	0.83[EUR][1000 genomes]
rs11950351	0.83[EUR][1000 genomes]
rs1370747	0.81[EUR][1000 genomes]
rs1370748	0.84[EUR][1000 genomes]
rs1438235	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1438237	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1438241	0.83[EUR][1000 genomes]
rs1561351	0.84[EUR][1000 genomes]
rs1561352	0.84[EUR][1000 genomes]
rs1561353	0.84[EUR][1000 genomes]
rs1561354	0.84[EUR][1000 genomes]
rs2218048	0.84[EUR][1000 genomes]
rs293643	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs293645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs402943	0.84[EUR][1000 genomes]
rs431521	0.84[EUR][1000 genomes]
rs432097	0.84[EUR][1000 genomes]
rs433863	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4362929	0.84[EUR][1000 genomes]
rs436407	0.83[EUR][1000 genomes]
rs4492099	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72782354	0.81[EUR][1000 genomes]
rs72782360	0.82[EUR][1000 genomes]
rs768177	0.83[EUR][1000 genomes]
rs7734840	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599285	chr5:105355890-106271223	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1016354	chr5:105752391-106392762	ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1017901	chr5:105847628-106298378	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1021423	chr5:105865862-106106525	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1032034	chr5:105975184-106104695	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1030118	chr5:106006097-106847949	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	esv2752055	chr5:106034797-106280515	Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv599297	chr5:106056347-106106521	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
9	esv2760928	chr5:106058868-106233117	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1020718	chr5:106058868-106293873	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs293638	PAM	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106066200-106067400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:106066400-106067400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links