Variant report

Variant	rs8020321
Chromosome Location	chr14:39535560-39535561
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1028591	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1040836	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12882909	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12883114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12883946	0.86[ASN][1000 genomes]
rs12887605	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12891260	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12891438	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12895569	0.84[ASN][1000 genomes]
rs12896384	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12896963	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12897263	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12897593	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17607605	0.86[ASN][1000 genomes]
rs17616347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17617123	0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17617289	0.92[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17670531	0.86[ASN][1000 genomes]
rs17676972	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17679493	0.86[CEU][hapmap];0.80[GIH][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1884383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884386	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1950508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1960796	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1980612	0.92[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs1980613	0.92[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs2038359	0.91[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2038360	0.81[EUR][1000 genomes]
rs2144526	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2144527	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2273315	0.96[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2415533	0.95[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2753596	0.85[CHB][hapmap];0.92[CHD][hapmap]
rs28364834	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34292075	0.86[ASN][1000 genomes]
rs34328534	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34870044	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34896803	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34984050	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35006421	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35270180	0.81[EUR][1000 genomes]
rs35395604	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35412542	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35502984	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35534904	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35729735	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35767652	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35873738	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35976812	0.80[EUR][1000 genomes]
rs4555056	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55902358	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55993688	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57550673	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59881143	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61338087	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6571887	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67190795	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67968129	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7140282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71407778	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7143056	0.86[ASN][1000 genomes]
rs7143370	0.85[ASN][1000 genomes]
rs7144730	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7145712	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7145856	0.92[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs7151407	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7152392	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715267	0.92[CEU][hapmap];0.90[CHB][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap]
rs7154223	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7157774	0.81[EUR][1000 genomes]
rs743222	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8007028	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8007240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8011244	0.91[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs8011494	0.92[CEU][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8017648	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8020013	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9743466	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9743749	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1038622	chr14:39423562-39604035	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv564417	chr14:39452317-39535560	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8020321	TRAPPC6B	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39521200-39535600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr14:39523800-39540200	Weak transcription	Psoas Muscle	Psoas
3	chr14:39525400-39540600	Strong transcription	NH-A	brain
4	chr14:39525600-39540600	Strong transcription	HSMM	muscle
5	chr14:39525600-39541000	Weak transcription	Brain Angular Gyrus	brain
6	chr14:39525600-39565600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr14:39526000-39537400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr14:39526000-39557200	Strong transcription	Osteobl	bone
9	chr14:39526400-39563200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr14:39526800-39537200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr14:39526800-39538400	Strong transcription	Liver	Liver
12	chr14:39526800-39540400	Weak transcription	Spleen	Spleen
13	chr14:39526800-39540800	Weak transcription	Right Ventricle	heart
14	chr14:39526800-39541200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr14:39526800-39552600	Weak transcription	Gastric	stomach
16	chr14:39526800-39553800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr14:39526800-39554000	Weak transcription	Aorta	Aorta
18	chr14:39526800-39554000	Weak transcription	Esophagus	oesophagus
19	chr14:39526800-39554200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr14:39526800-39554200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr14:39526800-39566600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr14:39527000-39536600	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr14:39527000-39537200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr14:39527000-39537200	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr14:39527000-39539000	Weak transcription	Lung	lung
26	chr14:39527000-39540600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr14:39527000-39540600	Weak transcription	Thymus	Thymus
28	chr14:39527000-39541800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr14:39527000-39554200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr14:39527000-39565400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr14:39527400-39536000	Strong transcription	Fetal Lung	lung
32	chr14:39527400-39536400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr14:39527400-39536600	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr14:39527400-39536600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr14:39527400-39537200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr14:39527400-39538200	Strong transcription	Duodenum Mucosa	Duodenum
37	chr14:39527400-39538400	Strong transcription	HepG2	liver
38	chr14:39527400-39549000	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr14:39527600-39554200	Weak transcription	K562	blood
40	chr14:39528000-39536600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr14:39528000-39547800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr14:39528000-39565400	Strong transcription	Placenta	Placenta
43	chr14:39528000-39565600	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr14:39528200-39536600	Strong transcription	Adipose Nuclei	Adipose
45	chr14:39528200-39537800	Strong transcription	Fetal Intestine Large	intestine
46	chr14:39528200-39545800	Strong transcription	Dnd41	blood
47	chr14:39528200-39548800	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr14:39528600-39566400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr14:39528800-39535600	Strong transcription	HUVEC	blood vessel
50	chr14:39529200-39559400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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