Variant report

Variant	rs5998233
Chromosome Location	chr22:32482321-32482322
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	22:32477762-32487457..22:32846948-32860159	Hela-S3	cervix:
2	22:31936958-31958600..22:32477762-32487457	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000214093	Chromatin interaction
ENSG00000184459	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1056444	0.87[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs130260	0.87[AMR][1000 genomes]
rs130261	0.87[AMR][1000 genomes]
rs130262	0.81[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs130266	0.92[ASW][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs130407	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs135020	1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs135021	0.81[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs135023	0.92[ASW][hapmap];0.81[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs135110	0.92[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs135111	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2246704	0.81[CEU][hapmap]
rs2413070	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2858753	0.81[CEU][hapmap]
rs3888536	0.86[CHB][hapmap]
rs4602316	0.86[CHB][hapmap]
rs4821004	0.81[CEU][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.82[YRI][hapmap]
rs4821014	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs5753843	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs5753852	1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs5994466	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5994468	0.88[CEU][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5998237	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5998253	0.86[CHB][hapmap]
rs7291239	0.90[EUR][1000 genomes]
rs739009	0.87[LWK][hapmap];1.00[YRI][hapmap]
rs8137665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8139657	0.86[CHB][hapmap]
rs93108	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9606906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609433	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609459	0.86[CHB][hapmap]

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	nsv1060529	chr22:32370432-32525699	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv834177	chr22:32416679-32594663	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	esv1803811	chr22:32441022-32509431	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv948789	chr22:32462505-32764760	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv1065175	chr22:32467617-32761093	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	nsv544680	chr22:32467617-32761093	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	esv2830423	chr22:32477718-32767825	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5998233	LARGE	cis	cerebellum	SCAN
rs5998233	CHEK2	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32469400-32489800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr22:32473400-32495000	Weak transcription	Colonic Mucosa	Colon
3	chr22:32473600-32495600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr22:32476200-32495800	Weak transcription	Stomach Mucosa	stomach
5	chr22:32476600-32499400	Weak transcription	Pancreas	Pancrea
6	chr22:32477600-32486200	Strong transcription	Duodenum Mucosa	Duodenum
7	chr22:32480000-32482400	Strong transcription	Fetal Intestine Small	intestine
8	chr22:32480000-32490400	Weak transcription	Spleen	Spleen
9	chr22:32480400-32484000	Strong transcription	Fetal Intestine Large	intestine
10	chr22:32481200-32482600	Genic enhancers	Left Ventricle	heart
11	chr22:32482200-32482600	Flanking Active TSS	Fetal Heart	heart
12	chr22:32482200-32482600	Genic enhancers	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links