Variant report

Variant	rs8104035
Chromosome Location	chr19:40184769-40184770
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr19:40184659-40184886	HepG2	liver:	n/a	chr19:40184782-40184793
2	USF1	chr19:40184682-40184960	H1-hESC	embryonic stem cell:	n/a	chr19:40184782-40184793

Variant related genes	Relation type
ENSG00000240320	TF binding region

Extended variants
information (count: 81 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1034867	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs10407647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10409279	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10410864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10755	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1126158	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17608	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2074926	0.89[JPT][hapmap]
rs2159169	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2159170	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2286759	0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs35837917	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs364911	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs367529	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs367788	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs372081	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs372902	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs373449	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs375867	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs378917	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs383768	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs384138	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs385240	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs385288	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs385520	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs388648	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs391646	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs391660	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs395892	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs396854	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs399641	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4028673	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs412884	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4132248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414423	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs416255	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs418664	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs425218	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs425265	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs428007	1.00[CEU][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs431329	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs437780	1.00[CEU][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs439881	1.00[CEU][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs440191	1.00[CEU][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs440334	1.00[CEU][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs44048	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs44049	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs444817	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs444963	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs446425	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs447034	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs453827	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4802054	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4803286	0.81[AFR][1000 genomes]
rs4830	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58602176	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61213408	0.82[AFR][1000 genomes]
rs6508903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249368	0.82[AFR][1000 genomes]
rs7249415	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7249575	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7250681	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7253094	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7254368	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7254761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7255025	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7255040	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7258833	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8102588	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:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057361	chr19:40123868-40310996	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1061361	chr19:40131820-40310996	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv579511	chr19:40132825-40310497	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1062394	chr19:40133229-40310186	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv544004	chr19:40133229-40310186	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv3355956	chr19:40135051-40188792	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	esv3998	chr19:40135120-40188646	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv3397881	chr19:40150495-40199437	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1059691	chr19:40168862-40306373	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv544005	chr19:40168862-40306373	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	esv3332670	chr19:40181720-40297955	Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs8104035	CEACAM21	cis	parietal	SCAN
rs8104035	BLVRB	cis	parietal	SCAN
rs8104035	PLD3	cis	parietal	SCAN
rs8104035	GLTSCR1	cis	parietal	SCAN
rs8104035	CEACAM8	cis	cerebellum	SCAN
rs8104035	FOXA3	cis	parietal	SCAN
rs8104035	ITPKC	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40171200-40189000	Weak transcription	Psoas Muscle	Psoas
2	chr19:40184400-40188000	Enhancers	HepG2	liver
3	chr19:40184600-40185000	Enhancers	H1 Cell Line	embryonic stem cell
4	chr19:40184600-40185200	Enhancers	H9 Cell Line	embryonic stem cell
5	chr19:40184600-40185200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:40184600-40185200	Enhancers	Placenta	Placenta
7	chr19:40184600-40186400	Weak transcription	GM12878-XiMat	blood

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