Variant report

Variant	rs1379115
Chromosome Location	chr5:59997886-59997887
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:59994810-59998074	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:59997848..60001535-chr5:60002216..60006200,5	K562	blood:
2	chr5:59995886..59998322-chr5:60239584..60242446,2	MCF-7	breast:
3	chr5:59996423..59998684-chr5:60001090..60003995,3	MCF-7	breast:

Variant related genes	Relation type
DEPDC1B	TF binding region
ENSG00000049167	Chromatin interaction
ENSG00000164182	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10043291	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs10050803	0.89[CEU][hapmap]
rs10054744	0.83[ASN][1000 genomes]
rs10058456	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs10069929	0.83[ASN][1000 genomes]
rs10440618	0.83[ASN][1000 genomes]
rs10471493	0.82[ASN][1000 genomes]
rs10805370	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs10939858	0.90[ASN][1000 genomes]
rs10939860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10939862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1117674	0.82[ASN][1000 genomes]
rs1117675	0.83[ASN][1000 genomes]
rs1117677	0.83[ASN][1000 genomes]
rs11739724	0.82[EUR][1000 genomes]
rs11740327	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs11741754	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11745627	0.83[EUR][1000 genomes]
rs11948543	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.95[YRI][hapmap];0.85[EUR][1000 genomes]
rs11952735	0.83[EUR][1000 genomes]
rs11954496	0.81[ASN][1000 genomes]
rs11955398	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11956023	0.88[EUR][1000 genomes]
rs11959922	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes]
rs12186391	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12514253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12515025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12517174	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12517207	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12522801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12655515	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12655977	0.83[ASN][1000 genomes]
rs1379114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1379116	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1379117	0.85[EUR][1000 genomes]
rs1444237	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs1456742	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1456743	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1460958	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs1562235	0.83[EUR][1000 genomes]
rs17387940	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1816899	0.83[EUR][1000 genomes]
rs1824120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1870014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1960479	0.83[ASN][1000 genomes]
rs1992612	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2045356	0.85[CEU][hapmap]
rs2061250	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs2085409	0.85[ASN][1000 genomes]
rs2085410	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2085411	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2085413	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2100584	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2198865	0.81[ASN][1000 genomes]
rs2409792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2409794	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs286153	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs286154	0.85[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap]
rs286158	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs2898287	0.83[EUR][1000 genomes]
rs2898288	0.85[ASN][1000 genomes]
rs3857236	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs3899221	0.83[ASN][1000 genomes]
rs4277863	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs4398599	0.83[ASN][1000 genomes]
rs4400080	0.83[ASN][1000 genomes]
rs4406099	0.81[ASN][1000 genomes]
rs4447941	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4524466	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4577661	0.83[ASN][1000 genomes]
rs4700380	0.85[EUR][1000 genomes]
rs4700384	0.83[ASN][1000 genomes]
rs4700388	0.81[ASN][1000 genomes]
rs55720622	0.83[EUR][1000 genomes]
rs55854817	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56191602	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56726435	0.97[ASN][1000 genomes]
rs57521726	0.81[EUR][1000 genomes]
rs62373024	0.83[EUR][1000 genomes]
rs62373025	0.82[EUR][1000 genomes]
rs6449483	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs6449485	0.81[EUR][1000 genomes]
rs6449487	0.85[EUR][1000 genomes]
rs6449490	0.81[ASN][1000 genomes]
rs6449491	0.81[ASN][1000 genomes]
rs6449493	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs6874072	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs6882727	0.81[ASN][1000 genomes]
rs6887434	0.83[ASN][1000 genomes]
rs6887637	0.81[ASN][1000 genomes]
rs755077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7701708	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7707698	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7720233	1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs7730342	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7736518	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs897672	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs930864	0.84[ASN][1000 genomes]
rs9654363	0.83[ASN][1000 genomes]
rs9686489	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9942410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	nsv4850	chr5:59976186-60039810	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	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
8	esv1816307	chr5:59992305-60012235	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
9	esv1794154	chr5:59995393-60012235	Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	esv1821070	chr5:59995393-60012235	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	esv1801919	chr5:59995393-60013913	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1379115	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59996600-59998200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:59996800-59998000	Enhancers	Fetal Intestine Small	intestine
3	chr5:59996800-60001800	Enhancers	Placenta	Placenta
4	chr5:59997000-59998000	Enhancers	HMEC	breast
5	chr5:59997000-59998000	Enhancers	K562	blood
6	chr5:59997000-59999600	Weak transcription	Stomach Mucosa	stomach

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