Variant report

Variant	rs4408422
Chromosome Location	chr13:40319257-40319258
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11147769	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11618960	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17591231	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17591266	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4133063	0.92[AFR][1000 genomes]
rs4245396	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4288869	0.92[AFR][1000 genomes]
rs4338665	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4384490	0.81[ASN][1000 genomes]
rs4403927	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4409964	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4941939	0.81[ASN][1000 genomes]
rs4941941	0.81[ASN][1000 genomes]
rs4943691	0.81[ASN][1000 genomes]
rs4943694	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4943695	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4943696	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7319128	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7325068	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7327824	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7330211	0.92[AFR][1000 genomes]
rs7332791	0.83[ASN][1000 genomes]
rs7334651	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7335799	0.82[ASN][1000 genomes]
rs7337585	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7984958	0.83[ASN][1000 genomes]
rs7998641	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8000009	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9315725	0.81[ASN][1000 genomes]
rs9315729	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9315730	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9532420	0.81[ASN][1000 genomes]
rs9532429	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9532432	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9532436	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9532439	0.80[AMR][1000 genomes]
rs9548880	0.81[ASN][1000 genomes]
rs9548893	0.82[ASN][1000 genomes]
rs9548894	0.83[ASN][1000 genomes]
rs9548896	0.82[ASN][1000 genomes]
rs9548898	0.92[AFR][1000 genomes]
rs9548900	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9548901	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548905	0.87[AFR][1000 genomes]
rs9548906	0.88[AFR][1000 genomes]
rs9548913	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9548914	0.86[AFR][1000 genomes]
rs9548916	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9548917	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9548918	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9548919	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9548920	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9548922	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9548926	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9548927	0.83[AFR][1000 genomes]
rs9548928	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548929	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9548930	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9566471	0.82[ASN][1000 genomes]
rs9566472	0.82[ASN][1000 genomes]
rs9566474	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576891	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9576892	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9576894	0.92[AFR][1000 genomes]
rs9576895	0.90[AFR][1000 genomes]
rs9576896	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576897	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576898	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][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	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1054797	chr13:40198744-40618428	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv541755	chr13:40198744-40618428	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv832586	chr13:40222880-40379063	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1040458	chr13:40249387-40638129	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv471130	chr13:40261945-40350912	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4408422	COG6	cis	Muscle Skeletal	GTEx
rs4408422	COG6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40255800-40340200	Weak transcription	Psoas Muscle	Psoas
2	chr13:40267600-40341200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr13:40274600-40327000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr13:40286200-40332200	Weak transcription	Esophagus	oesophagus
5	chr13:40290600-40328600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr13:40293000-40340800	Weak transcription	Colon Smooth Muscle	Colon
7	chr13:40293600-40329000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr13:40294200-40339200	Weak transcription	Fetal Brain Male	brain
9	chr13:40294600-40327800	Weak transcription	NH-A	brain
10	chr13:40297600-40339800	Weak transcription	Brain Hippocampus Middle	brain
11	chr13:40297800-40329800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr13:40299200-40327600	Weak transcription	Fetal Heart	heart
13	chr13:40302000-40328800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr13:40304000-40328800	Weak transcription	Dnd41	blood
15	chr13:40304600-40340000	Weak transcription	Osteobl	bone
16	chr13:40306400-40327400	Weak transcription	HUVEC	blood vessel
17	chr13:40306600-40325200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr13:40307600-40329400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr13:40309200-40331400	Weak transcription	Stomach Mucosa	stomach
20	chr13:40309200-40334600	Weak transcription	HepG2	liver
21	chr13:40311400-40324000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr13:40311400-40347200	Weak transcription	HSMM	muscle
23	chr13:40311600-40324200	Weak transcription	Adipose Nuclei	Adipose
24	chr13:40311600-40326600	Weak transcription	Placenta	Placenta
25	chr13:40311600-40329400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr13:40311600-40331200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr13:40311600-40339800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr13:40311600-40340000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr13:40311800-40331000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr13:40311800-40339800	Weak transcription	Brain Anterior Caudate	brain
31	chr13:40311800-40340000	Weak transcription	Ovary	ovary
32	chr13:40312000-40325800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr13:40312000-40340000	Weak transcription	Brain Angular Gyrus	brain
34	chr13:40312200-40325600	Weak transcription	Liver	Liver
35	chr13:40312200-40325800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr13:40312200-40326000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr13:40312200-40327000	Weak transcription	Primary T cells from cord blood	blood
38	chr13:40312200-40327000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr13:40312200-40327400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr13:40312200-40329000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr13:40312200-40329800	Weak transcription	Aorta	Aorta
42	chr13:40312200-40331800	Weak transcription	Left Ventricle	heart
43	chr13:40312200-40333000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr13:40312200-40340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr13:40312200-40340000	Weak transcription	Pancreas	Pancrea
46	chr13:40312200-40340200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr13:40312200-40351200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr13:40312400-40325000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr13:40312400-40325000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr13:40312400-40325400	Weak transcription	Fetal Muscle Trunk	muscle

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