Variant report

Variant	rs17780860
Chromosome Location	chr5:58623098-58623099
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11744760	0.84[EUR][1000 genomes]
rs12186633	1.00[CHD][hapmap]
rs17528543	1.00[CHD][hapmap]
rs17528550	1.00[CHD][hapmap]
rs17723785	1.00[CHD][hapmap]
rs17724250	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17780836	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2194210	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs72767722	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17780860	DEPDC1B	cis	parietal	SCAN

Chromatin state (count:30 , 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	chr5:58614000-58624600	Weak transcription	Fetal Stomach	stomach
5	chr5:58616200-58624600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr5:58617600-58624600	Weak transcription	Left Ventricle	heart
7	chr5:58618600-58624600	Weak transcription	Right Atrium	heart
8	chr5:58618800-58623200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:58618800-58624400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:58618800-58629000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr5:58619200-58624000	Weak transcription	Fetal Kidney	kidney
12	chr5:58619200-58624200	Weak transcription	Hela-S3	cervix
13	chr5:58619200-58624400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:58619400-58625400	Weak transcription	Fetal Intestine Large	intestine
15	chr5:58620800-58623200	Weak transcription	Colon Smooth Muscle	Colon
16	chr5:58621200-58624200	Weak transcription	Fetal Intestine Small	intestine
17	chr5:58621400-58626200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr5:58622200-58623400	Enhancers	Fetal Heart	heart
19	chr5:58622200-58625000	Enhancers	Fetal Brain Male	brain
20	chr5:58622200-58625400	Enhancers	Fetal Lung	lung
21	chr5:58622400-58624000	Enhancers	A549	lung
22	chr5:58622600-58623400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr5:58622600-58623400	Enhancers	Fetal Brain Female	brain
24	chr5:58622800-58623600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:58622800-58623600	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr5:58622800-58625000	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr5:58623000-58623200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:58623000-58623400	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr5:58623000-58623400	Enhancers	Fetal Muscle Leg	muscle
30	chr5:58623000-58623400	Enhancers	Psoas Muscle	Psoas

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