Variant report

Variant	rs945240
Chromosome Location	chr20:16588308-16588309
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1105853	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2207205	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2328049	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4813228	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4813229	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4813230	0.94[EUR][1000 genomes]
rs4814513	1.00[EUR][1000 genomes]
rs4814516	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4814517	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6034549	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6034552	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6034554	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6044161	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6044162	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6044169	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6044170	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6044171	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6044173	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6044174	0.93[EUR][1000 genomes]
rs6075081	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6080303	0.81[CHB][hapmap];0.83[TSI][hapmap]
rs6080312	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6080315	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6080317	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6080320	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6080330	0.96[EUR][1000 genomes]
rs6111200	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6135800	0.81[CHB][hapmap]
rs6135809	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs928624	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs945239	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[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	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	nsv470542	chr20:16567202-16588308	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
3	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
4	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
5	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs945240	C20orf23	Cis_1M	lymphoblastoid	RTeQTL
rs945240	KIF16B	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

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

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