Variant report

Variant	rs6080322
Chromosome Location	chr20:16589003-16589004
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12481403	0.85[AMR][1000 genomes]
rs17681978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6075068	0.84[MEX][hapmap]
rs6075069	0.84[MEX][hapmap]
rs6075076	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6075083	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6080314	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6080326	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057674	chr20:16564642-16593209	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
2	nsv1055217	chr20:16568062-16596470	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv458942	chr20:16568129-16589003	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
4	nsv585653	chr20:16568129-16589003	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6080322	MGC44328	cis	parietal	SCAN
rs6080322	SEC23B	cis	parietal	SCAN
rs6080322	KIF16B	cis	parietal	SCAN
rs6080322	PARP6	trans	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16587000-16593200	Enhancers	Fetal Intestine Large	intestine
2	chr20:16587400-16589600	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr20:16587400-16589600	Enhancers	Small Intestine	intestine
4	chr20:16587400-16589800	Enhancers	Fetal Kidney	kidney
5	chr20:16587400-16590000	Enhancers	Adipose Nuclei	Adipose
6	chr20:16587400-16590600	Enhancers	Fetal Brain Male	brain
7	chr20:16587600-16589200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
8	chr20:16587600-16589400	Enhancers	Stomach Smooth Muscle	stomach
9	chr20:16587800-16589800	Enhancers	Fetal Brain Female	brain
10	chr20:16587800-16590400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr20:16587800-16590600	Enhancers	Fetal Lung	lung
12	chr20:16588000-16589200	Enhancers	Colon Smooth Muscle	Colon
13	chr20:16588000-16589600	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr20:16588000-16589800	Enhancers	Fetal Muscle Leg	muscle
15	chr20:16588000-16592400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr20:16588200-16589200	Enhancers	Stomach Mucosa	stomach
17	chr20:16588200-16590400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr20:16588400-16589200	Enhancers	Colonic Mucosa	Colon
19	chr20:16588600-16590000	Enhancers	Right Atrium	heart
20	chr20:16588800-16589200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr20:16588800-16589400	Enhancers	HSMMtube	muscle
22	chr20:16588800-16590400	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr20:16588800-16590800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr20:16589000-16589200	Bivalent Enhancer	HepG2	liver
25	chr20:16589000-16589600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr20:16589000-16589800	Enhancers	Liver	Liver
27	chr20:16589000-16589800	Enhancers	Duodenum Mucosa	Duodenum
28	chr20:16589000-16589800	Weak transcription	Ovary	ovary
29	chr20:16589000-16589800	Weak transcription	Pancreas	Pancrea
30	chr20:16589000-16589800	Weak transcription	Right Ventricle	heart
31	chr20:16589000-16590200	Weak transcription	Left Ventricle	heart
32	chr20:16589000-16592600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr20:16589000-16593000	Enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links