Variant report

Variant	rs3851792
Chromosome Location	chr17:45059824-45059825
allele	A/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	FOXA1	chr17:45059812-45060455	HepG2	liver:	n/a	n/a
2	FOXA2	chr17:45059721-45060541	HepG2	liver:	n/a	n/a
3	FOXA1	chr17:45059823-45060277	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45055112..45057937-chr17:45059099..45061766,2	MCF-7	breast:
2	chr17:45020840..45022921-chr17:45057973..45060223,2	K562	blood:

Variant related genes	Relation type
RPRML	TF binding region
ENSG00000263142	Chromatin interaction
ENSG00000179673	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11079745	0.83[CEU][hapmap]
rs11079747	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11079750	0.87[CEU][hapmap];0.98[GIH][hapmap];0.89[TSI][hapmap]
rs11653589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11658863	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11869840	0.83[CEU][hapmap];0.80[TSI][hapmap]
rs12938690	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12949446	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12952596	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1476498	0.83[JPT][hapmap]
rs1634265	0.83[JPT][hapmap]
rs1713493	0.83[JPT][hapmap]
rs2316758	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851786	0.82[CEU][hapmap]
rs3851795	1.00[ASN][1000 genomes]
rs3851796	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851798	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851799	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074249	0.87[CEU][hapmap]
rs4572469	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4968286	0.83[CEU][hapmap]
rs4968304	0.87[CEU][hapmap]
rs6504622	0.83[CEU][hapmap]
rs8068715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8071243	0.83[JPT][hapmap]
rs858677	0.83[JPT][hapmap]
rs9889762	0.83[CEU][hapmap];0.80[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3492820	chr17:44174959-45161556	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3492821	chr17:44174959-45161556	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3502492	chr17:44305975-45169159	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv3502493	chr17:44305975-45169159	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv531823	chr17:44485771-45067769	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv908562	chr17:44828931-45102413	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv949295	chr17:44836653-45080757	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
8	nsv833466	chr17:45020360-45204537	Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3851792	IFI35	cis	parietal	SCAN
rs3851792	MRPL10	cis	parietal	SCAN
rs3851792	LRRC46	cis	parietal	SCAN
rs3851792	ARL17P1	cis	multi-tissue	Pritchard
rs3851792	C17orf53	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45056800-45069000	Weak transcription	Gastric	stomach
2	chr17:45057000-45061200	Weak transcription	Pancreas	Pancrea
3	chr17:45057000-45065600	Weak transcription	Brain Substantia Nigra	brain
4	chr17:45057000-45078400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr17:45057200-45086800	Weak transcription	Right Atrium	heart
6	chr17:45057200-45100000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr17:45057800-45082400	Weak transcription	Brain Angular Gyrus	brain
8	chr17:45058200-45060400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr17:45058600-45060000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr17:45058800-45060000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:45058800-45061200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr17:45059000-45060400	Weak transcription	Primary B cells from peripheral blood	blood
13	chr17:45059400-45065000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr17:45059600-45060200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr17:45059600-45060200	Enhancers	HepG2	liver
16	chr17:45059800-45060000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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