Variant report

Variant	rs6419420
Chromosome Location	chr12:85835047-85835048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10746344	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10746346	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10746347	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10779161	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10779164	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10779167	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10779168	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10779169	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10779170	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10779173	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10779180	0.83[ASN][1000 genomes]
rs10779181	0.82[ASN][1000 genomes]
rs10779182	0.80[ASN][1000 genomes]
rs10862979	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10862990	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10862991	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10862993	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10862999	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10863000	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10863007	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10863008	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10863032	0.80[ASN][1000 genomes]
rs11116807	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11116832	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11116833	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11116930	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11116934	0.83[ASN][1000 genomes]
rs11116935	0.83[ASN][1000 genomes]
rs11831266	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11835161	0.82[ASN][1000 genomes]
rs12578708	0.84[ASN][1000 genomes]
rs1398440	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1398442	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1870933	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1870935	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2199508	0.81[ASN][1000 genomes]
rs2199511	0.82[ASN][1000 genomes]
rs2199512	0.82[ASN][1000 genomes]
rs2199513	0.84[ASN][1000 genomes]
rs2199516	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2199517	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2199518	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2219711	0.82[ASN][1000 genomes]
rs2405248	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2405254	0.84[ASN][1000 genomes]
rs2405256	0.82[ASN][1000 genomes]
rs2405257	0.80[ASN][1000 genomes]
rs4761063	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4897817	0.83[ASN][1000 genomes]
rs4897825	0.82[ASN][1000 genomes]
rs6419421	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6539899	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6539901	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6539902	0.82[ASN][1000 genomes]
rs7133064	0.82[ASN][1000 genomes]
rs7133855	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7134486	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7136236	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7295445	0.82[ASN][1000 genomes]
rs7297262	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7302629	0.82[ASN][1000 genomes]
rs7303316	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7304475	0.80[ASN][1000 genomes]
rs7316167	0.84[ASN][1000 genomes]
rs7485084	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7485590	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7486767	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7487599	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7955601	0.80[ASN][1000 genomes]
rs7957797	0.98[ASN][1000 genomes]
rs7973153	0.80[ASN][1000 genomes]
rs7973323	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7977259	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs898986	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9788015	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9788074	0.81[EUR][1000 genomes];0.89[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	esv1792335	chr12:85321249-86003609	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv817242	chr12:85622245-86069213	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1054573	chr12:85658602-86235433	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised 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	16 gene(s)	inside rSNPs	diseases
4	nsv1035600	chr12:85661373-86235433	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6419420	RASSF9	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:85833000-85836000	Enhancers	Fetal Intestine Large	intestine
2	chr12:85833200-85836000	Enhancers	Fetal Intestine Small	intestine
3	chr12:85833400-85836200	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr12:85833800-85836000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:85833800-85839000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:85833800-85839000	Weak transcription	Colonic Mucosa	Colon
7	chr12:85834400-85836000	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr12:85834600-85835200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:85834600-85835400	Weak transcription	Stomach Mucosa	stomach
10	chr12:85834600-85835600	Enhancers	A549	lung
11	chr12:85834800-85835200	Enhancers	Small Intestine	intestine
12	chr12:85834800-85836000	Enhancers	Duodenum Mucosa	Duodenum

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