Variant report

Variant	rs17122567
Chromosome Location	chr12:48413875-48413876
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48406038..48410831-chr12:48411860..48418424,9	MCF-7	breast:
2	chr12:48391315..48400584-chr12:48411914..48418489,16	MCF-7	breast:
3	chr12:48407869..48410123-chr12:48411477..48413880,2	K562	blood:
4	chr12:48399203..48400811-chr12:48412734..48415114,2	K562	blood:
5	chr12:48410357..48413530-chr12:48413703..48417962,3	K562	blood:

Variant related genes	Relation type
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10450783	0.89[EUR][1000 genomes]
rs10492082	0.85[ASN][1000 genomes]
rs1049392	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs10747529	1.00[JPT][hapmap]
rs10875733	0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10875739	1.00[JPT][hapmap]
rs10875752	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs10875754	1.00[JPT][hapmap]
rs10875761	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs10875766	1.00[JPT][hapmap]
rs11168350	0.90[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs11168353	0.90[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11168354	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11168358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168361	0.88[ASN][1000 genomes]
rs11168363	0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11168364	0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11168373	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11168404	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs11168417	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs11168424	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs11168434	1.00[JPT][hapmap]
rs11168435	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs11168438	1.00[JPT][hapmap]
rs11168445	1.00[JPT][hapmap]
rs11168448	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs11168453	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs11168454	1.00[JPT][hapmap]
rs12228924	0.87[GIH][hapmap]
rs12422355	1.00[JPT][hapmap]
rs12423250	0.90[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs1859440	0.81[ASN][1000 genomes]
rs1859442	0.96[ASN][1000 genomes]
rs1859443	0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs1978161	0.82[JPT][hapmap]
rs2056448	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2240306	0.81[ASN][1000 genomes]
rs2286020	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs2408954	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3742075	0.93[JPT][hapmap]
rs3825403	1.00[JPT][hapmap]
rs4258439	1.00[JPT][hapmap]
rs58086963	0.96[ASN][1000 genomes]
rs59667534	0.85[ASN][1000 genomes]
rs6580658	0.80[JPT][hapmap]
rs7134203	0.91[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs7134878	0.95[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs7135261	0.82[YRI][hapmap]
rs7299704	1.00[JPT][hapmap]
rs7302354	1.00[JPT][hapmap]
rs7303677	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs733592	0.81[ASN][1000 genomes]
rs7484942	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs765260	1.00[JPT][hapmap]
rs7962390	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs7962569	0.88[GIH][hapmap];0.94[JPT][hapmap]
rs8181670	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs886589	1.00[JPT][hapmap]
rs954326	0.90[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap]
rs9651981	0.90[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs9804751	0.90[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2760677	chr12:48412410-48416967	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17122567	DDN	cis	parietal	SCAN
rs17122567	TMEM106C	cis	parietal	SCAN
rs17122567	ZNF641	cis	Muscle Skeletal	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48399400-48415000	Weak transcription	Right Atrium	heart
2	chr12:48410600-48414800	Weak transcription	Hela-S3	cervix
3	chr12:48411600-48415000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:48411600-48415200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:48412000-48415800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr12:48412400-48415000	Weak transcription	Fetal Intestine Large	intestine
7	chr12:48412400-48415000	Weak transcription	Fetal Intestine Small	intestine
8	chr12:48412400-48415000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr12:48412600-48415400	Weak transcription	HepG2	liver
10	chr12:48413600-48415400	Weak transcription	Right Ventricle	heart

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