Variant report

Variant	rs1677193
Chromosome Location	chr12:31756155-31756156
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31741885..31745117-chr12:31755313..31758226,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170456	Chromatin interaction
ENSG00000255867	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10771833	0.84[CEU][hapmap];0.89[CHB][hapmap]
rs10843953	0.84[CEU][hapmap];0.95[CHB][hapmap]
rs10843957	0.84[CEU][hapmap];0.95[CHB][hapmap]
rs10843966	0.80[ASN][1000 genomes]
rs10843968	0.85[ASN][1000 genomes]
rs10843969	0.86[ASN][1000 genomes]
rs10843971	0.87[ASN][1000 genomes]
rs11051428	0.84[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap]
rs11051446	0.80[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap]
rs11051454	0.81[ASN][1000 genomes]
rs11051461	0.82[ASN][1000 genomes]
rs11051467	0.87[CEU][hapmap];0.85[ASN][1000 genomes]
rs11051472	0.87[ASN][1000 genomes]
rs11051476	0.83[CEU][hapmap]
rs11051478	0.86[EUR][1000 genomes]
rs1150949	0.80[ASN][1000 genomes]
rs12371432	0.81[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap]
rs1259360	0.80[ASN][1000 genomes]
rs1268747	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[TSI][hapmap]
rs16918740	0.85[ASN][1000 genomes]
rs1879385	0.82[ASN][1000 genomes]
rs2351921	0.84[CEU][hapmap]
rs2351922	0.83[CEU][hapmap];0.95[CHB][hapmap]
rs3741878	0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap]
rs3803114	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs3850966	0.85[ASN][1000 genomes]
rs3887250	0.83[CEU][hapmap];0.89[CHB][hapmap]
rs4930979	0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap]
rs4931499	0.84[CEU][hapmap];0.95[CHB][hapmap]
rs4931512	0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap]
rs4931513	0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap]
rs6487995	0.87[ASN][1000 genomes]
rs7132688	0.82[CEU][hapmap];0.94[CHB][hapmap]
rs7297507	0.81[ASN][1000 genomes]
rs7297997	0.84[CEU][hapmap];0.89[CHB][hapmap]
rs7300106	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs7302695	0.81[ASN][1000 genomes]
rs7313889	0.84[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap]
rs7314404	0.84[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap]
rs7960380	0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[ASN][1000 genomes]
rs7980274	0.85[EUR][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	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1797962	chr12:31733044-31761172	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1677193	DENND5B	cis	parietal	SCAN
rs1677193	DENND5B	cis	cerebellum	SCAN
rs1677193	YARS2	cis	cerebellum	SCAN
rs1677193	REP15	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31745400-31760400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:31750200-31758000	Enhancers	Primary B cells from peripheral blood	blood
3	chr12:31752800-31757200	Enhancers	Primary B cells from cord blood	blood
4	chr12:31753800-31756400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:31756000-31756400	Flanking Active TSS	GM12878-XiMat	blood

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