Variant report

Variant	rs9576885
Chromosome Location	chr13:40243386-40243387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12584772	0.81[AMR][1000 genomes]
rs4329796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4346098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4570710	0.91[CEU][hapmap];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];0.91[ASN][1000 genomes]
rs7989518	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7994943	0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs9315726	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9532423	0.82[AMR][1000 genomes]
rs9548849	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9548874	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9548882	1.00[CEU][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9548886	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548887	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9548889	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548890	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9548892	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9548902	0.81[AMR][1000 genomes]
rs9548903	0.81[AMR][1000 genomes]
rs9548925	0.80[AMR][1000 genomes]
rs9566464	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9566468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576878	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9576879	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9576883	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576886	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];0.94[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9576885	COG6	cis	multi-tissue	Pritchard
rs9576885	COG6	Cis_1M	lymphoblastoid	RTeQTL

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	chr13:40230800-40246600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr13:40230800-40254600	Weak transcription	Left Ventricle	heart
8	chr13:40230800-40254600	Weak transcription	Psoas Muscle	Psoas
9	chr13:40230800-40254800	Weak transcription	Fetal Thymus	thymus
10	chr13:40230800-40256400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr13:40230800-40258400	Weak transcription	Colonic Mucosa	Colon
12	chr13:40230800-40262000	Weak transcription	Thymus	Thymus
13	chr13:40230800-40275000	Weak transcription	Right Ventricle	heart
14	chr13:40231000-40243800	Weak transcription	Fetal Heart	heart
15	chr13:40231000-40252200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr13:40231000-40252800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr13:40231000-40254400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr13:40231000-40254400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr13:40231000-40254600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr13:40231000-40254600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr13:40231000-40254600	Weak transcription	NHLF	lung
22	chr13:40231000-40256400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr13:40231000-40256400	Weak transcription	NHEK	skin
24	chr13:40231000-40257200	Weak transcription	HMEC	breast
25	chr13:40231000-40261800	Weak transcription	Brain Substantia Nigra	brain
26	chr13:40231000-40266200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr13:40231000-40270800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr13:40231000-40286000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr13:40231200-40254400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr13:40231200-40254600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr13:40231200-40254800	Weak transcription	Fetal Stomach	stomach
32	chr13:40231400-40253600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr13:40231400-40254600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr13:40231400-40264200	Weak transcription	Esophagus	oesophagus
35	chr13:40231400-40268000	Weak transcription	Small Intestine	intestine
36	chr13:40231600-40254400	Weak transcription	Fetal Brain Male	brain
37	chr13:40231600-40270200	Weak transcription	Gastric	stomach
38	chr13:40231800-40252000	Weak transcription	Brain Angular Gyrus	brain
39	chr13:40232000-40251600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr13:40232000-40252800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr13:40232000-40253200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr13:40232000-40254600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr13:40232200-40252000	Weak transcription	Colon Smooth Muscle	Colon
44	chr13:40233000-40254600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr13:40233000-40273600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr13:40233000-40295600	Weak transcription	Pancreas	Pancrea
47	chr13:40233200-40253400	Weak transcription	HepG2	liver
48	chr13:40233200-40254600	Weak transcription	Brain Hippocampus Middle	brain
49	chr13:40233400-40243400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr13:40233600-40244000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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