Variant report

Variant	rs4682323
Chromosome Location	chr3:111597750-111597751
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10934118	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10934119	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10934121	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11922171	0.90[EUR][1000 genomes]
rs13064071	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13070728	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1500045	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1500046	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2055364	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4682322	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6767186	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6781879	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6786077	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6789911	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6805339	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6805359	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7649418	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv980070	chr3:111592547-111602240	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4682323	PHLDB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111584600-111603400	Weak transcription	Fetal Intestine Large	intestine
2	chr3:111585200-111622000	Weak transcription	HSMMtube	muscle
3	chr3:111585400-111603400	Weak transcription	Spleen	Spleen
4	chr3:111585400-111609000	Weak transcription	Esophagus	oesophagus
5	chr3:111587200-111603000	Weak transcription	Placenta	Placenta
6	chr3:111587800-111599200	Weak transcription	Liver	Liver
7	chr3:111589200-111598400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:111589200-111603400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:111589800-111603400	Weak transcription	Pancreas	Pancrea
10	chr3:111591400-111598400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:111591600-111598400	Weak transcription	Right Atrium	heart
12	chr3:111591600-111603200	Weak transcription	Ovary	ovary
13	chr3:111591600-111603600	Weak transcription	HepG2	liver
14	chr3:111591600-111610600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:111591600-111633200	Weak transcription	Fetal Kidney	kidney
16	chr3:111593400-111599600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:111593400-111601400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:111593600-111598200	Weak transcription	Adipose Nuclei	Adipose
19	chr3:111593600-111598800	Weak transcription	Aorta	Aorta
20	chr3:111593600-111599000	Weak transcription	Left Ventricle	heart
21	chr3:111593600-111599200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:111593600-111601400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:111593600-111603000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:111593600-111603000	Weak transcription	Lung	lung
25	chr3:111593600-111603200	Weak transcription	Gastric	stomach
26	chr3:111593600-111603400	Weak transcription	HSMM	muscle
27	chr3:111593600-111608800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr3:111593800-111598800	Weak transcription	Hela-S3	cervix
29	chr3:111593800-111599000	Weak transcription	A549	lung
30	chr3:111593800-111599000	Weak transcription	NH-A	brain
31	chr3:111593800-111599200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:111593800-111601200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:111593800-111602000	Weak transcription	HUVEC	blood vessel
34	chr3:111593800-111602800	Weak transcription	NHLF	lung
35	chr3:111593800-111603000	Weak transcription	Fetal Stomach	stomach
36	chr3:111593800-111603200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:111593800-111603400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr3:111594000-111598600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:111594000-111603400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr3:111594400-111603200	Weak transcription	HMEC	breast
41	chr3:111595200-111598200	Weak transcription	Right Ventricle	heart
42	chr3:111595200-111601200	Weak transcription	NHEK	skin
43	chr3:111595400-111601200	Weak transcription	Osteobl	bone
44	chr3:111595400-111602600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:111595600-111598200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:111595800-111598400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:111595800-111599000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links