Variant report

Variant	rs3909863
Chromosome Location	chr19:51318909-51318910
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	NFYA	chr19:51318570-51319047	K562	blood:	n/a	chr19:51318910-51318928
2	USF2	chr19:51318744-51319055	K562	blood:	n/a	chr19:51318867-51318878 chr19:51318933-51318944
3	CBX3	chr19:51318479-51319129	K562	blood:	n/a	n/a
4	USF2	chr19:51318785-51319081	GM12878	blood:	n/a	chr19:51318867-51318878 chr19:51318933-51318944
5	USF1	chr19:51318706-51319054	SK-N-SH	brain:	n/a	chr19:51318866-51318877
6	USF1	chr19:51318688-51319037	A549	lung:	n/a	chr19:51318866-51318877
7	NFYB	chr19:51318658-51319076	K562	blood:	n/a	chr19:51318916-51318931 chr19:51318849-51318864
8	USF1	chr19:51318721-51319111	H1-hESC	embryonic stem cell:	n/a	chr19:51318866-51318877
9	USF1	chr19:51318702-51319055	K562	blood:	n/a	chr19:51318866-51318877
10	USF1	chr19:51318659-51319063	ECC-1	luminal epithelium:	n/a	chr19:51318866-51318877
11	USF1	chr19:51318653-51319127	ECC-1	luminal epithelium:	n/a	chr19:51318866-51318877
12	USF2	chr19:51318731-51319055	H1-hESC	embryonic stem cell:	n/a	chr19:51318867-51318878 chr19:51318933-51318944
13	USF1	chr19:51318578-51319153	K562	blood:	n/a	chr19:51318866-51318877
14	MAX	chr19:51318766-51319059	H1-hESC	embryonic stem cell:	n/a	n/a
15	USF1	chr19:51318788-51318976	HepG2	liver:	n/a	chr19:51318866-51318877
16	NFYB	chr19:51318734-51319047	Hela-S3	cervix:	n/a	chr19:51318916-51318931 chr19:51318849-51318864
17	USF1	chr19:51318671-51319058	A549	lung:	n/a	chr19:51318866-51318877
18	USF1	chr19:51318773-51318956	HepG2	liver:	n/a	chr19:51318866-51318877
19	USF1	chr19:51318627-51319120	H1-hESC	embryonic stem cell:	n/a	chr19:51318866-51318877
20	USF1	chr19:51318695-51319129	A549	lung:	n/a	chr19:51318866-51318877
21	USF1	chr19:51318794-51319013	SK-N-SH_RA	brain:	n/a	chr19:51318866-51318877
22	USF2	chr19:51318766-51319059	Hela-S3	cervix:	n/a	chr19:51318867-51318878 chr19:51318933-51318944
23	NFYA	chr19:51318677-51319031	GM12878	blood:	n/a	chr19:51318910-51318928
24	USF1	chr19:51318712-51319078	A549	lung:	n/a	chr19:51318866-51318877
25	NFYB	chr19:51318672-51319115	GM12878	blood:	n/a	chr19:51318916-51318931 chr19:51318849-51318864
26	ATF3	chr19:51318762-51318982	K562	blood:	n/a	n/a
27	USF1	chr19:51318587-51319176	HCT-116	colon:	n/a	chr19:51318866-51318877

No.	Distal block	Cell Line	Cell type
1	chr19:51306338..51308122-chr19:51317273..51319351,3	MCF-7	breast:
2	chr19:51313105..51316231-chr19:51316664..51319784,4	MCF-7	breast:
3	chr19:51317461..51319588-chr19:51332509..51335386,2	K562	blood:
4	chr19:51317814..51320322-chr19:51337524..51339862,2	K562	blood:
5	chr19:51317914..51322870-chr19:51325257..51328084,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180279	TF binding region
ENSG00000167747	Chromatin interaction
ENSG00000267968	Chromatin interaction
ENSG00000167748	Chromatin interaction
ENSG00000174562	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10853825	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11668998	0.86[CHD][hapmap]
rs12052047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17800513	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2288417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2288418	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3212810	0.84[MKK][hapmap]
rs3212820	0.90[ASN][1000 genomes]
rs3212833	0.97[ASN][1000 genomes]
rs3212834	0.97[ASN][1000 genomes]
rs3212835	0.97[ASN][1000 genomes]
rs3212836	0.97[ASN][1000 genomes]
rs3212840	0.96[ASN][1000 genomes]
rs3212846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3745522	0.86[MKK][hapmap];1.00[YRI][hapmap]
rs3745528	0.83[CHD][hapmap]
rs4801853	0.86[CHD][hapmap]
rs4802741	0.83[CHD][hapmap]
rs4802742	0.86[CHD][hapmap]
rs5517	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs5519	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs55859860	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56840371	0.94[AFR][1000 genomes]
rs56914577	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58095696	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58844524	0.94[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs59300606	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62114335	0.94[AFR][1000 genomes]
rs62115586	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9991	0.86[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060760	chr19:50883425-51463712	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1058177	chr19:50984774-51463712	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv912288	chr19:51283791-51334355	Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
4	nsv912289	chr19:51283791-51335943	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
5	nsv912290	chr19:51283791-51344483	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
6	nsv526232	chr19:51301230-51335943	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
7	nsv519121	chr19:51308092-51332670	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3909863	KLK1	cis	brain	seeQTL
rs3909863	EGFL6	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51318800-51319200	Weak transcription	K562	blood

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