Variant report

Variant	rs2322687
Chromosome Location	chr4:20741823-20741824
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10031524	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10938803	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11936560	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11940062	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1820505	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2114474	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3816874	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4577580	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61428210	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6447971	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6447972	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6447973	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6811933	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6857386	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6858843	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7663837	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7668797	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7688592	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7689421	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7694208	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs964019	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010145	chr4:20601908-21057992	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv537052	chr4:20601908-21057992	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv829876	chr4:20638736-20835621	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv869522	chr4:20724433-20938248	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2322687	PACRGL	cis	lung	GTEx
rs2322687	C4orf28	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20724600-20742000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr4:20725000-20753000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:20730600-20757600	Weak transcription	HSMM	muscle
4	chr4:20732600-20758400	Weak transcription	Brain Angular Gyrus	brain
5	chr4:20736000-20747800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr4:20738600-20742000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
7	chr4:20738800-20742000	Weak transcription	NHDF-Ad	bronchial
8	chr4:20739200-20748200	Weak transcription	Psoas Muscle	Psoas
9	chr4:20739200-20761200	Weak transcription	Fetal Heart	heart
10	chr4:20739600-20755200	Weak transcription	K562	blood
11	chr4:20740200-20742200	Weak transcription	Osteobl	bone
12	chr4:20740200-20755200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:20740600-20742800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr4:20740600-20743400	Weak transcription	Brain Hippocampus Middle	brain
15	chr4:20740600-20754800	Weak transcription	Dnd41	blood
16	chr4:20740600-20756600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr4:20740600-20757200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr4:20740600-20763600	Weak transcription	Brain Anterior Caudate	brain
19	chr4:20740800-20742800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr4:20740800-20746400	Weak transcription	Left Ventricle	heart
21	chr4:20740800-20750800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr4:20740800-20751400	Weak transcription	Pancreas	Pancrea
23	chr4:20740800-20756000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:20740800-20757200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:20740800-20757600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:20740800-20763600	Weak transcription	HSMMtube	muscle
27	chr4:20740800-20770600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr4:20740800-20791200	Weak transcription	Ovary	ovary
29	chr4:20741000-20749200	Weak transcription	Fetal Stomach	stomach
30	chr4:20741000-20753600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:20741000-20757800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr4:20741600-20754200	Weak transcription	Fetal Lung	lung
33	chr4:20741600-20756200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:20741800-20757400	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links