Variant report

Variant	rs7692397
Chromosome Location	chr4:88226533-88226534
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr4:88225649-88226546	A549	lung:	n/a	n/a
2	MAFK	chr4:88225717-88226545	Hela-S3	cervix:	n/a	n/a
3	TCF12	chr4:88225626-88226533	A549	lung:	n/a	n/a
4	STAT3	chr4:88225826-88226610	Hela-S3	cervix:	n/a	n/a
5	FOXM1	chr4:88225661-88226647	MCF-7	breast:	n/a	n/a
6	GATA3	chr4:88225620-88226575	MCF-7	breast:	n/a	n/a
7	GATA3	chr4:88225597-88226753	MCF-7	breast:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:88226132..88228278-chr4:88229243..88230944,2	MCF-7	breast:
2	chr4:88224415..88227242-chr4:88231505..88233396,2	K562	blood:
3	chr4:88225790..88227669-chr4:88236912..88239118,2	MCF-7	breast:
4	chr4:88225793..88228433-chr4:88233021..88235909,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR5705	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10004269	0.83[AFR][1000 genomes]
rs10028612	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10084835	0.83[LWK][hapmap];0.89[YRI][hapmap]
rs10222732	0.92[CHB][hapmap]
rs13108668	0.89[YRI][hapmap]
rs28658397	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35663073	0.85[AFR][1000 genomes]
rs3923441	0.81[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs3923442	0.89[YRI][hapmap]
rs4134363	0.83[CEU][hapmap];0.92[CHB][hapmap];0.80[AMR][1000 genomes]
rs4345139	0.94[YRI][hapmap]
rs4352444	0.94[YRI][hapmap]
rs4435708	0.82[AFR][1000 genomes]
rs4693812	0.83[AFR][1000 genomes]
rs6531967	0.84[AFR][1000 genomes]
rs6531971	0.91[ASN][1000 genomes]
rs6531978	0.85[CHB][hapmap]
rs6816742	0.89[YRI][hapmap]
rs6836489	0.84[AFR][1000 genomes]
rs6857133	0.83[CHB][hapmap]
rs6858253	0.98[AFR][1000 genomes]
rs72873623	0.84[AFR][1000 genomes]
rs7668929	0.87[YRI][hapmap]
rs7684895	0.81[AFR][1000 genomes]
rs7699556	0.89[YRI][hapmap]
rs9991773	1.00[CHB][hapmap]
rs9992481	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1007020	chr4:88046263-88235018	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537169	chr4:88046263-88235018	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv516203	chr4:88167878-88228228	Enhancers Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv870296	chr4:88173534-88295927	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv470050	chr4:88186509-88228228	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
7	esv2760913	chr4:88194170-88228412	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
8	nsv879527	chr4:88194170-88250203	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
9	esv1802846	chr4:88211056-88246450	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7692397	HSD17B13	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88225400-88237800	Strong transcription	Liver	Liver
2	chr4:88225800-88227200	Active TSS	Hela-S3	cervix
3	chr4:88226000-88226600	Active TSS	A549	lung
4	chr4:88226200-88226600	Active TSS	Aorta	Aorta
5	chr4:88226200-88226800	Active TSS	NHEK	skin
6	chr4:88226400-88231600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links