Variant report

Variant	rs4346098
Chromosome Location	chr13:40256483-40256484
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12584772	0.83[AMR][1000 genomes]
rs4329796	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4570710	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4603426	0.82[AMR][1000 genomes]
rs56322803	0.81[AMR][1000 genomes]
rs6563745	0.81[AMR][1000 genomes]
rs7988187	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7989518	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7994943	0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs9315726	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9532423	0.84[AMR][1000 genomes]
rs9532427	0.80[AMR][1000 genomes]
rs9548849	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9548874	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9548882	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9548886	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548887	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9548889	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548890	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9548892	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548899	0.81[AMR][1000 genomes]
rs9548902	0.83[AMR][1000 genomes]
rs9548903	0.83[AMR][1000 genomes]
rs9548904	0.81[AMR][1000 genomes]
rs9548925	0.82[AMR][1000 genomes]
rs9566464	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9566468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576878	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9576879	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9576883	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576885	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]
rs9576886	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]
rs9576888	0.96[AMR][1000 genomes];0.99[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
rs4346098	COG6	cis	multi-tissue	Pritchard
rs4346098	COG6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40230600-40263800	Weak transcription	Spleen	Spleen
2	chr13:40230800-40258400	Weak transcription	Colonic Mucosa	Colon
3	chr13:40230800-40262000	Weak transcription	Thymus	Thymus
4	chr13:40230800-40275000	Weak transcription	Right Ventricle	heart
5	chr13:40231000-40257200	Weak transcription	HMEC	breast
6	chr13:40231000-40261800	Weak transcription	Brain Substantia Nigra	brain
7	chr13:40231000-40266200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr13:40231000-40270800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr13:40231000-40286000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr13:40231400-40264200	Weak transcription	Esophagus	oesophagus
11	chr13:40231400-40268000	Weak transcription	Small Intestine	intestine
12	chr13:40231600-40270200	Weak transcription	Gastric	stomach
13	chr13:40233000-40273600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr13:40233000-40295600	Weak transcription	Pancreas	Pancrea
15	chr13:40236800-40261600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr13:40238000-40291600	Weak transcription	Fetal Intestine Small	intestine
17	chr13:40238600-40261600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr13:40240600-40257000	Weak transcription	Brain Germinal Matrix	brain
19	chr13:40241200-40261600	Weak transcription	HSMM	muscle
20	chr13:40246200-40262800	Weak transcription	Fetal Heart	heart
21	chr13:40246400-40297400	Weak transcription	HUVEC	blood vessel
22	chr13:40251200-40258200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr13:40251400-40257800	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr13:40251600-40257200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr13:40251600-40257600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr13:40251600-40258400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr13:40252000-40257600	Strong transcription	Primary B cells from peripheral blood	blood
28	chr13:40252000-40257600	Strong transcription	Fetal Intestine Large	intestine
29	chr13:40252000-40258000	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr13:40252000-40258200	Strong transcription	Fetal Lung	lung
31	chr13:40252200-40257800	Strong transcription	Placenta	Placenta
32	chr13:40252200-40258200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr13:40252200-40258200	Strong transcription	Adipose Nuclei	Adipose
34	chr13:40252200-40261800	Weak transcription	K562	blood
35	chr13:40252400-40257400	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr13:40252400-40257800	Strong transcription	Primary B cells from cord blood	blood
37	chr13:40253000-40258200	Strong transcription	NHDF-Ad	bronchial
38	chr13:40253000-40266200	Weak transcription	Colon Smooth Muscle	Colon
39	chr13:40253200-40257600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr13:40253400-40266600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr13:40253800-40256600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr13:40254200-40256800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr13:40254400-40257800	Strong transcription	Fetal Kidney	kidney
44	chr13:40254400-40257800	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr13:40254400-40258200	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr13:40254600-40264000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr13:40254800-40257000	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr13:40255000-40257400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr13:40255000-40257400	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr13:40255000-40257800	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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