Variant report

Variant	rs9576886
Chromosome Location	chr13:40252030-40252031
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12584772	0.81[AMR][1000 genomes]
rs4329796	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4346098	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4570710	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4603426	0.80[AMR][1000 genomes]
rs7988187	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7989518	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7994943	0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs9315726	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9532423	0.82[AMR][1000 genomes]
rs9548849	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9548874	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9548882	0.86[CHB][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9548886	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548887	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9548889	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548890	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9548892	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548902	0.81[AMR][1000 genomes]
rs9548903	0.81[AMR][1000 genomes]
rs9548925	0.80[AMR][1000 genomes]
rs9566464	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9566468	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576878	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9576879	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9576883	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576885	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576888	0.98[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	nsv870429	chr13:40235061-40265634	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9576886	COG6	Cis_1M	lymphoblastoid	RTeQTL
rs9576886	COG6	cis	multi-tissue	Pritchard

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40230600-40252200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:40230600-40254600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:40230600-40254600	Weak transcription	Lung	lung
4	chr13:40230600-40254800	Weak transcription	Aorta	Aorta
5	chr13:40230600-40263800	Weak transcription	Spleen	Spleen
6	chr13:40230800-40254600	Weak transcription	Left Ventricle	heart
7	chr13:40230800-40254600	Weak transcription	Psoas Muscle	Psoas
8	chr13:40230800-40254800	Weak transcription	Fetal Thymus	thymus
9	chr13:40230800-40256400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr13:40230800-40258400	Weak transcription	Colonic Mucosa	Colon
11	chr13:40230800-40262000	Weak transcription	Thymus	Thymus
12	chr13:40230800-40275000	Weak transcription	Right Ventricle	heart
13	chr13:40231000-40252200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr13:40231000-40252800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr13:40231000-40254400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr13:40231000-40254400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr13:40231000-40254600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr13:40231000-40254600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr13:40231000-40254600	Weak transcription	NHLF	lung
20	chr13:40231000-40256400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr13:40231000-40256400	Weak transcription	NHEK	skin
22	chr13:40231000-40257200	Weak transcription	HMEC	breast
23	chr13:40231000-40261800	Weak transcription	Brain Substantia Nigra	brain
24	chr13:40231000-40266200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr13:40231000-40270800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr13:40231000-40286000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr13:40231200-40254400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr13:40231200-40254600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr13:40231200-40254800	Weak transcription	Fetal Stomach	stomach
30	chr13:40231400-40253600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr13:40231400-40254600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr13:40231400-40264200	Weak transcription	Esophagus	oesophagus
33	chr13:40231400-40268000	Weak transcription	Small Intestine	intestine
34	chr13:40231600-40254400	Weak transcription	Fetal Brain Male	brain
35	chr13:40231600-40270200	Weak transcription	Gastric	stomach
36	chr13:40232000-40252800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr13:40232000-40253200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr13:40232000-40254600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr13:40233000-40254600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr13:40233000-40273600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr13:40233000-40295600	Weak transcription	Pancreas	Pancrea
42	chr13:40233200-40253400	Weak transcription	HepG2	liver
43	chr13:40233200-40254600	Weak transcription	Brain Hippocampus Middle	brain
44	chr13:40233600-40254200	Weak transcription	Fetal Brain Female	brain
45	chr13:40233800-40254600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr13:40234800-40254400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr13:40235600-40252800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr13:40235600-40254400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr13:40235800-40254600	Weak transcription	NH-A	brain
50	chr13:40236000-40252200	Weak transcription	Rectal Mucosa Donor 31	rectum

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