Variant report

Variant	rs3923441
Chromosome Location	chr4:88189651-88189652
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:88140123..88141719-chr4:88189481..88191440,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145332	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10084835	0.89[YRI][hapmap]
rs11097130	0.90[JPT][hapmap]
rs12649023	0.81[CHB][hapmap]
rs13108668	0.81[LWK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs13112695	0.81[CHB][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs13149842	0.96[ASN][1000 genomes]
rs3923442	0.84[LWK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs4331742	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4345139	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4352444	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6531975	0.81[CHB][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs6531977	0.81[CHB][hapmap]
rs6816742	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs6858253	0.84[AFR][1000 genomes]
rs7668929	0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs7672465	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7688962	0.81[CHB][hapmap]
rs7692397	0.81[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7698613	0.83[AFR][1000 genomes]
rs7698974	0.82[ASN][1000 genomes]
rs7699556	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]

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	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	nsv537171	chr4:88182433-88209309	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3923441	PPM1K	cis	cerebellum	SCAN
rs3923441	HSD17B11	cis	parietal	SCAN
rs3923441	C19orf22	trans	parietal	SCAN
rs3923441	PKD2	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88184600-88191400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:88188800-88190000	Enhancers	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links