Variant report

Variant	rs653349
Chromosome Location	chr3:109621619-109621620
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1164205	0.91[ASN][1000 genomes]
rs1164206	0.91[ASN][1000 genomes]
rs2693621	0.82[ASN][1000 genomes]
rs2693634	0.81[ASN][1000 genomes]
rs2700237	0.81[ASN][1000 genomes]
rs2950151	0.81[ASN][1000 genomes]
rs2950152	0.81[ASN][1000 genomes]
rs581999	0.88[ASN][1000 genomes]
rs582946	0.88[ASN][1000 genomes]
rs586783	0.83[ASN][1000 genomes]
rs591010	0.82[ASN][1000 genomes]
rs591350	0.85[ASN][1000 genomes]
rs593904	0.81[ASN][1000 genomes]
rs595732	0.81[ASN][1000 genomes]
rs598795	0.81[ASN][1000 genomes]
rs598837	0.81[ASN][1000 genomes]
rs599684	0.81[ASN][1000 genomes]
rs600581	0.81[ASN][1000 genomes]
rs600604	0.81[ASN][1000 genomes]
rs601036	0.81[ASN][1000 genomes]
rs601561	0.84[ASN][1000 genomes]
rs603474	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs604088	0.82[ASN][1000 genomes]
rs605795	0.90[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs607450	0.88[ASN][1000 genomes]
rs610419	0.81[ASN][1000 genomes]
rs614845	0.81[ASN][1000 genomes]
rs617480	0.82[ASN][1000 genomes]
rs619279	0.90[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs620464	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs620727	0.82[ASN][1000 genomes]
rs636972	0.81[ASN][1000 genomes]
rs638718	0.88[ASN][1000 genomes]
rs640194	0.82[ASN][1000 genomes]
rs642142	0.81[ASN][1000 genomes]
rs652762	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs652972	0.89[ASN][1000 genomes]
rs655376	0.88[ASN][1000 genomes]
rs656615	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs656888	0.91[ASN][1000 genomes]
rs662181	0.81[ASN][1000 genomes]
rs662417	0.84[ASN][1000 genomes]
rs666016	0.82[ASN][1000 genomes]
rs667006	0.81[ASN][1000 genomes]
rs671520	0.81[ASN][1000 genomes]
rs679711	0.85[ASN][1000 genomes]
rs686100	0.81[ASN][1000 genomes]
rs686694	0.90[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs687239	0.90[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs687619	0.90[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs687962	0.81[ASN][1000 genomes]
rs689213	0.81[ASN][1000 genomes]
rs776341	0.81[ASN][1000 genomes]
rs776343	0.84[ASN][1000 genomes]
rs776344	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009075	chr3:109462019-109800029	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv591270	chr3:109462400-109793785	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1011265	chr3:109474218-109625143	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv877332	chr3:109575764-110186611	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1009550	chr3:109577315-109795453	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv1839660	chr3:109591203-109678542	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv829666	chr3:109593745-109768652	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv2754434	chr3:109604310-109777310	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs653349	CD96	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:109618600-109621800	Enhancers	Dnd41	blood
2	chr3:109621200-109622200	Weak transcription	Rectal Mucosa Donor 31	rectum

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