Variant report

Variant	rs1824159
Chromosome Location	chr5:58618644-58618645
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58618629..58620597-chr5:58633400..58635092,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10036406	0.90[CEU][hapmap]
rs10055446	0.89[CEU][hapmap]
rs10060200	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064893	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs10068836	0.81[CEU][hapmap]
rs10070436	0.81[CEU][hapmap]
rs10079396	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10079614	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10079932	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740402	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs13328160	0.83[CEU][hapmap]
rs13328175	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs13328226	0.83[CEU][hapmap]
rs13354210	0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17528285	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs17528473	0.83[CEU][hapmap]
rs17528634	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs17724250	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17780213	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs17780584	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes]
rs17780740	0.90[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17780836	1.00[JPT][hapmap]
rs2044419	0.84[EUR][1000 genomes]
rs2194210	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs56183128	0.84[EUR][1000 genomes]
rs57516309	0.87[EUR][1000 genomes]
rs72765993	0.87[EUR][1000 genomes]
rs72767710	0.84[EUR][1000 genomes]
rs72767722	0.95[EUR][1000 genomes]
rs9292201	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs9716677	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598252	chr5:58487764-58618889	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1030117	chr5:58587672-58637179	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv2760953	chr5:58609468-58620440	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1824159	DEPDC1B	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58612800-58627200	Weak transcription	Aorta	Aorta
2	chr5:58613600-58626600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:58613600-58628600	Weak transcription	Gastric	stomach
4	chr5:58613800-58619800	Weak transcription	Psoas Muscle	Psoas
5	chr5:58613800-58622600	Weak transcription	Fetal Brain Female	brain
6	chr5:58614000-58624600	Weak transcription	Fetal Stomach	stomach
7	chr5:58616200-58618800	Weak transcription	Fetal Brain Male	brain
8	chr5:58616200-58623000	Weak transcription	Fetal Muscle Leg	muscle
9	chr5:58616200-58624600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr5:58616800-58618800	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr5:58616800-58619000	Enhancers	Duodenum Mucosa	Duodenum
12	chr5:58616800-58619200	Enhancers	Fetal Kidney	kidney
13	chr5:58616800-58619200	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr5:58616800-58621600	Enhancers	Fetal Heart	heart
15	chr5:58617000-58618800	Enhancers	Rectal Smooth Muscle	rectum
16	chr5:58617000-58618800	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr5:58617000-58619200	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr5:58617000-58620200	Enhancers	Colon Smooth Muscle	Colon
19	chr5:58617200-58622600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:58617400-58619200	Enhancers	Hela-S3	cervix
21	chr5:58617400-58620000	Enhancers	A549	lung
22	chr5:58617600-58624600	Weak transcription	Left Ventricle	heart
23	chr5:58618000-58618800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr5:58618000-58618800	Enhancers	Small Intestine	intestine
25	chr5:58618000-58619400	Enhancers	Fetal Intestine Large	intestine
26	chr5:58618400-58619000	Enhancers	Fetal Intestine Small	intestine
27	chr5:58618600-58618800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr5:58618600-58618800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr5:58618600-58618800	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr5:58618600-58619200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:58618600-58620000	Weak transcription	Fetal Lung	lung
32	chr5:58618600-58624600	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links