Variant report

Variant	rs3810398
Chromosome Location	chr19:40187343-40187344
allele	A/C
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	FOS	chr19:40187116-40187439	MCF10A-Er-Src	breast:	n/a	chr19:40187265-40187275 chr19:40187266-40187275 chr19:40187265-40187274 chr19:40187265-40187275 chr19:40187266-40187273 chr19:40187264-40187276
2	RFX5	chr19:40187046-40187501	Hela-S3	cervix:	n/a	n/a
3	TCF7L2	chr19:40187087-40187437	Hela-S3	cervix:	n/a	chr19:40187265-40187274
4	RAD21	chr19:40187091-40187438	Hela-S3	cervix:	n/a	n/a
5	FOS	chr19:40187082-40187487	MCF10A-Er-Src	breast:	n/a	chr19:40187265-40187275 chr19:40187266-40187275 chr19:40187265-40187274 chr19:40187265-40187275 chr19:40187266-40187273 chr19:40187264-40187276
6	CEBPB	chr19:40187072-40187467	MCF-7	breast:	n/a	chr19:40187330-40187342
7	FOS	chr19:40187092-40187447	MCF10A-Er-Src	breast:	n/a	chr19:40187265-40187275 chr19:40187266-40187275 chr19:40187265-40187274 chr19:40187265-40187275 chr19:40187266-40187273 chr19:40187264-40187276
8	FOXA1	chr19:40187095-40187454	HepG2	liver:	n/a	n/a
9	STAT3	chr19:40187184-40187384	MCF10A-Er-Src	breast:	n/a	chr19:40187265-40187274
10	FOSL2	chr19:40187065-40187428	MCF-7	breast:	n/a	chr19:40187265-40187275 chr19:40187266-40187275 chr19:40187265-40187274 chr19:40187265-40187275 chr19:40187266-40187273 chr19:40187263-40187274 chr19:40187264-40187276
11	CEBPB	chr19:40186892-40187546	Hela-S3	cervix:	n/a	chr19:40187330-40187342
12	JUND	chr19:40187095-40187458	HepG2	liver:	n/a	chr19:40187265-40187275 chr19:40187266-40187275 chr19:40187265-40187274 chr19:40187264-40187275 chr19:40187265-40187275 chr19:40187266-40187273 chr19:40187264-40187276
13	MXI1	chr19:40187145-40187538	Hela-S3	cervix:	n/a	n/a
14	FOS	chr19:40187083-40187453	MCF10A-Er-Src	breast:	n/a	chr19:40187265-40187275 chr19:40187266-40187275 chr19:40187265-40187274 chr19:40187265-40187275 chr19:40187266-40187273 chr19:40187264-40187276
15	FOXA1	chr19:40187063-40187444	HepG2	liver:	n/a	n/a
16	FOSL2	chr19:40187053-40187416	HepG2	liver:	n/a	chr19:40187265-40187275 chr19:40187266-40187275 chr19:40187265-40187274 chr19:40187265-40187275 chr19:40187266-40187273 chr19:40187263-40187274 chr19:40187264-40187276
17	FOXA2	chr19:40186154-40187603	HepG2	liver:	n/a	n/a
18	TEAD4	chr19:40187031-40187531	HepG2	liver:	n/a	n/a
19	FOXA1	chr19:40187063-40187436	HepG2	liver:	n/a	n/a
20	PRDM1	chr19:40186924-40187433	Hela-S3	cervix:	n/a	chr19:40187063-40187077 chr19:40187265-40187274 chr19:40187063-40187076 chr19:40187266-40187275 chr19:40187062-40187077 chr19:40187067-40187076
21	FOXA1	chr19:40186992-40187463	HepG2	liver:	n/a	n/a
22	EP300	chr19:40187054-40187555	Hela-S3	cervix:	n/a	chr19:40187266-40187275 chr19:40187059-40187073
23	STAT3	chr19:40187165-40187413	MCF10A-Er-Src	breast:	n/a	chr19:40187265-40187274
24	JUN	chr19:40187054-40187521	Hela-S3	cervix:	n/a	chr19:40187265-40187275 chr19:40187266-40187275 chr19:40187265-40187274 chr19:40187265-40187275 chr19:40187266-40187273 chr19:40187264-40187276
25	JUN	chr19:40187121-40187389	HepG2	liver:	n/a	chr19:40187265-40187275 chr19:40187266-40187275 chr19:40187265-40187274 chr19:40187265-40187275 chr19:40187266-40187273 chr19:40187264-40187276
26	FOS	chr19:40187114-40187458	Hela-S3	cervix:	n/a	chr19:40187265-40187275 chr19:40187266-40187275 chr19:40187265-40187274 chr19:40187265-40187275 chr19:40187266-40187273 chr19:40187264-40187276
27	JUND	chr19:40186999-40187650	Hela-S3	cervix:	n/a	chr19:40187265-40187275 chr19:40187266-40187275 chr19:40187265-40187274 chr19:40187264-40187275 chr19:40187265-40187275 chr19:40187266-40187273 chr19:40187264-40187276
28	MYC	chr19:40187167-40187453	MCF10A-Er-Src	breast:	n/a	n/a
29	CEBPB	chr19:40187146-40187415	HepG2	liver:	n/a	chr19:40187330-40187342
30	FOSL2	chr19:40187045-40187426	HepG2	liver:	n/a	chr19:40187265-40187275 chr19:40187266-40187275 chr19:40187265-40187274 chr19:40187265-40187275 chr19:40187266-40187273 chr19:40187263-40187274 chr19:40187264-40187276
31	STAT3	chr19:40187116-40187460	Hela-S3	cervix:	n/a	chr19:40187265-40187274
32	RCOR1	chr19:40187002-40187530	Hela-S3	cervix:	n/a	n/a
33	USF2	chr19:40187182-40187349	Hela-S3	cervix:	n/a	n/a
34	FOXA2	chr19:40187071-40187382	HepG2	liver:	n/a	n/a
35	JUND	chr19:40187140-40187352	HepG2	liver:	n/a	chr19:40187265-40187275 chr19:40187266-40187275 chr19:40187265-40187274 chr19:40187264-40187275 chr19:40187265-40187275 chr19:40187266-40187273 chr19:40187264-40187276
36	JUND	chr19:40187130-40187420	HepG2	liver:	n/a	chr19:40187265-40187275 chr19:40187266-40187275 chr19:40187265-40187274 chr19:40187264-40187275 chr19:40187265-40187275 chr19:40187266-40187273 chr19:40187264-40187276

Variant related genes	Relation type
ENSG00000240320	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11083533	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1126159	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11880813	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12461697	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12978229	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16973566	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16973568	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28625546	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35876063	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3786939	0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3810397	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55796830	0.98[ASN][1000 genomes]
rs55824044	0.99[ASN][1000 genomes]
rs56227027	0.81[ASN][1000 genomes]
rs56280894	0.96[ASN][1000 genomes]
rs56332617	0.99[ASN][1000 genomes]
rs56741478	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59661491	0.99[ASN][1000 genomes]
rs60447868	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60688354	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60714140	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71356866	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72480730	0.99[ASN][1000 genomes]
rs72480731	1.00[ASN][1000 genomes]
rs7251304	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7251631	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7259169	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7259291	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9789262	0.99[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3810398	ITPKC	cis	cerebellum	SCAN
rs3810398	POU2F2	cis	cerebellum	SCAN
rs3810398	PLA2G4C	cis	cerebellum	SCAN
rs3810398	ZNF574	cis	parietal	SCAN

Chromatin state (count:5 , 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	chr19:40186400-40187400	Enhancers	GM12878-XiMat	blood
4	chr19:40186400-40188400	Enhancers	Placenta	Placenta
5	chr19:40187200-40187600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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