Variant report

Variant	rs10402840
Chromosome Location	chr19:40187290-40187291
allele	A/G
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	POLR2A	chr19:40187145-40187328	GM12878	blood:	n/a	n/a
17	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
18	FOXA2	chr19:40186154-40187603	HepG2	liver:	n/a	n/a
19	TEAD4	chr19:40187031-40187531	HepG2	liver:	n/a	n/a
20	FOXA1	chr19:40187063-40187436	HepG2	liver:	n/a	n/a
21	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
22	FOXA1	chr19:40186992-40187463	HepG2	liver:	n/a	n/a
23	EP300	chr19:40187054-40187555	Hela-S3	cervix:	n/a	chr19:40187266-40187275 chr19:40187059-40187073
24	STAT3	chr19:40187165-40187413	MCF10A-Er-Src	breast:	n/a	chr19:40187265-40187274
25	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
26	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
27	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
28	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
29	MYC	chr19:40187167-40187453	MCF10A-Er-Src	breast:	n/a	n/a
30	CEBPB	chr19:40187146-40187415	HepG2	liver:	n/a	chr19:40187330-40187342
31	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
32	STAT3	chr19:40187116-40187460	Hela-S3	cervix:	n/a	chr19:40187265-40187274
33	RCOR1	chr19:40187002-40187530	Hela-S3	cervix:	n/a	n/a
34	USF2	chr19:40187182-40187349	Hela-S3	cervix:	n/a	n/a
35	FOXA2	chr19:40187071-40187382	HepG2	liver:	n/a	n/a
36	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
37	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: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10401663	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10402453	0.85[AMR][1000 genomes]
rs10416344	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10418762	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10420367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10422546	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10423105	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10423951	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10424853	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs10426447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13344252	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13344487	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16973564	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16973571	0.85[AMR][1000 genomes]
rs16973572	0.85[AMR][1000 genomes]
rs16973576	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28414506	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28491346	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28631884	0.83[AMR][1000 genomes]
rs28873117	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58503187	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58988184	0.85[AMR][1000 genomes]
rs59155776	0.85[AMR][1000 genomes]
rs60598133	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7253880	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73555896	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73557809	0.95[AFR][1000 genomes]
rs73557816	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73557827	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73557829	0.92[AMR][1000 genomes]
rs73557856	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8105258	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8112575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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

No data

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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