Variant report

Variant	rs13153359
Chromosome Location	chr5:60045247-60045248
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10057004	0.93[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs10805370	0.93[CHB][hapmap]
rs10939863	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs10939874	0.81[CEU][hapmap]
rs12655515	0.93[CHB][hapmap]
rs12696975	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13186761	1.00[CEU][hapmap];0.83[JPT][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13358053	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1445292	0.85[GIH][hapmap];0.81[TSI][hapmap]
rs158916	0.81[CEU][hapmap]
rs158920	0.81[CEU][hapmap]
rs158928	0.81[CEU][hapmap]
rs16878397	1.00[CEU][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes]
rs1824531	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2085412	0.87[ASN][1000 genomes]
rs2306350	0.81[CEU][hapmap]
rs2306351	0.81[CEU][hapmap]
rs2409796	0.98[ASN][1000 genomes]
rs28766005	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4235480	0.89[ASN][1000 genomes]
rs4307050	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4370226	0.84[ASN][1000 genomes]
rs4458532	0.98[ASN][1000 genomes]
rs4647078	0.81[CEU][hapmap]
rs4647108	0.81[CEU][hapmap]
rs4647168	0.81[CEU][hapmap]
rs4700385	0.89[ASN][1000 genomes]
rs4700387	0.86[ASN][1000 genomes]
rs4700392	0.81[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap]
rs6449483	1.00[CHB][hapmap]
rs6449484	1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs6449489	0.89[ASN][1000 genomes]
rs6449502	0.81[CEU][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs6449509	0.81[CEU][hapmap]
rs6449510	0.81[CEU][hapmap]
rs6869332	0.81[CEU][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap]
rs6871557	0.81[CEU][hapmap]
rs6874072	1.00[CHB][hapmap]
rs6876346	0.80[EUR][1000 genomes]
rs6877849	0.81[CEU][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs6881713	0.86[YRI][hapmap]
rs6891519	1.00[YRI][hapmap]
rs702564	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704338	0.93[CHB][hapmap]
rs7712473	0.81[CEU][hapmap];0.85[GIH][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs7714071	0.81[CEU][hapmap]
rs7719611	0.93[CHB][hapmap]
rs7719726	0.80[CHB][hapmap]
rs897672	1.00[CHB][hapmap]

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	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv462198	chr5:59969015-60116613	Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv598298	chr5:59969015-60116613	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1023403	chr5:59969534-60079822	Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv508362	chr5:59990308-60050894	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv934153	chr5:60004982-60309751	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	esv2763456	chr5:60007355-60151767	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
8	nsv1026190	chr5:60020156-60148535	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv537769	chr5:60020156-60148535	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
10	esv2752073	chr5:60034475-60136626	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13153359	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL
rs13153359	CWC27	cis	parietal	SCAN
rs13153359	NDUFAF2	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60037400-60047600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr5:60040800-60066600	Weak transcription	Fetal Intestine Small	intestine
3	chr5:60042200-60050000	Weak transcription	Fetal Intestine Large	intestine
4	chr5:60042200-60052000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr5:60042600-60055800	Weak transcription	Brain Hippocampus Middle	brain
6	chr5:60044000-60046200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr5:60044800-60046000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:60044800-60081600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr5:60044800-60098000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr5:60045000-60056600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:60045200-60048800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:60045200-60065000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:60045200-60084400	Weak transcription	Brain Angular Gyrus	brain

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