Variant report

Variant	rs58078456
Chromosome Location	chr5:60133707-60133708
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:60132825..60135249-chr5:60136200..60138330,2	K562	blood:
2	chr5:60131900..60133961-chr5:60138518..60140783,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164181	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1021005	0.92[ASN][1000 genomes]
rs10805374	0.81[ASN][1000 genomes]
rs10939879	0.81[ASN][1000 genomes]
rs11739952	0.80[ASN][1000 genomes]
rs11740632	0.91[ASN][1000 genomes]
rs12516995	0.81[ASN][1000 genomes]
rs12517310	0.82[ASN][1000 genomes]
rs12652830	0.81[ASN][1000 genomes]
rs12652878	0.92[ASN][1000 genomes]
rs12654306	0.92[ASN][1000 genomes]
rs12655603	0.90[ASN][1000 genomes]
rs13189346	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1382917	0.80[ASN][1000 genomes]
rs1471488	0.81[ASN][1000 genomes]
rs1479645	0.81[ASN][1000 genomes]
rs17332824	0.92[ASN][1000 genomes]
rs17392014	0.92[ASN][1000 genomes]
rs17419290	0.80[ASN][1000 genomes]
rs1867597	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2120956	0.86[ASN][1000 genomes]
rs2120957	0.92[ASN][1000 genomes]
rs28436304	0.80[ASN][1000 genomes]
rs2898309	0.81[ASN][1000 genomes]
rs34741733	0.93[ASN][1000 genomes]
rs3797559	0.88[ASN][1000 genomes]
rs4642318	0.80[ASN][1000 genomes]
rs4647052	0.82[ASN][1000 genomes]
rs4647132	0.92[ASN][1000 genomes]
rs4647137	0.93[ASN][1000 genomes]
rs4647150	0.91[ASN][1000 genomes]
rs4700397	0.93[ASN][1000 genomes]
rs4700398	0.95[EUR][1000 genomes]
rs4700399	0.91[ASN][1000 genomes]
rs4700402	0.81[ASN][1000 genomes]
rs4700404	0.80[ASN][1000 genomes]
rs55738840	0.81[ASN][1000 genomes]
rs55814394	0.81[ASN][1000 genomes]
rs56031340	0.80[ASN][1000 genomes]
rs60858663	0.90[ASN][1000 genomes]
rs61017995	0.81[ASN][1000 genomes]
rs61101592	0.92[ASN][1000 genomes]
rs62365455	0.80[ASN][1000 genomes]
rs62365458	0.81[ASN][1000 genomes]
rs62367862	0.81[ASN][1000 genomes]
rs62367872	0.80[ASN][1000 genomes]
rs62367879	0.81[ASN][1000 genomes]
rs62367885	0.80[ASN][1000 genomes]
rs62367903	0.80[ASN][1000 genomes]
rs62372102	0.85[ASN][1000 genomes]
rs62372103	0.91[ASN][1000 genomes]
rs62372133	0.90[ASN][1000 genomes]
rs62372134	0.90[ASN][1000 genomes]
rs67490467	0.80[ASN][1000 genomes]
rs67555188	0.91[ASN][1000 genomes]
rs67858932	0.91[ASN][1000 genomes]
rs6884966	0.92[ASN][1000 genomes]
rs726824	0.80[ASN][1000 genomes]
rs72757187	0.80[ASN][1000 genomes]
rs72759206	0.80[ASN][1000 genomes]
rs7700975	0.80[AMR][1000 genomes]
rs7701398	0.92[ASN][1000 genomes]
rs7709522	0.83[ASN][1000 genomes]
rs7714071	0.83[AMR][1000 genomes]
rs7717909	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7722373	0.83[ASN][1000 genomes]
rs7723349	0.80[ASN][1000 genomes]
rs7723901	0.81[ASN][1000 genomes]
rs7731760	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs868791	0.81[ASN][1000 genomes]
rs9687099	0.92[ASN][1000 genomes]
rs976630	0.88[ASN][1000 genomes]
rs976631	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	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
3	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
4	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
5	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
6	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
7	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv1017095	chr5:60050600-60414783	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv933326	chr5:60074031-60413061	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv881712	chr5:60116613-60266875	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv881713	chr5:60116613-60305125	Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv598305	chr5:60116613-60308836	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv881714	chr5:60116613-60313015	Bivalent Enhancer Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv881715	chr5:60116613-60356423	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv598306	chr5:60129361-60266875	Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv598307	chr5:60129361-60308836	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv881716	chr5:60129361-60313015	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	nsv462199	chr5:60129361-60329624	Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
19	nsv598308	chr5:60129361-60329624	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58078456	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60102200-60137800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:60129400-60137200	Weak transcription	Fetal Intestine Small	intestine
3	chr5:60131200-60134600	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr5:60131600-60134000	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr5:60131600-60134400	Enhancers	H1 Cell Line	embryonic stem cell
6	chr5:60131600-60134400	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr5:60131800-60134200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
8	chr5:60131800-60134400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr5:60132000-60133800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:60132000-60138600	Weak transcription	HMEC	breast
11	chr5:60132400-60133800	Weak transcription	NHEK	skin
12	chr5:60132400-60138600	Weak transcription	A549	lung
13	chr5:60133000-60134000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr5:60133000-60134000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr5:60133000-60134200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr5:60133000-60134600	Enhancers	K562	blood
17	chr5:60133400-60133800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr5:60133400-60134600	Enhancers	Fetal Intestine Large	intestine
19	chr5:60133600-60134200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:60133600-60134400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr5:60133600-60134400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:60133600-60134400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:60133600-60134400	Enhancers	Gastric	stomach
24	chr5:60133600-60134400	Enhancers	Pancreas	Pancrea

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