Variant report

Variant	rs4261404
Chromosome Location	chr13:40242648-40242649
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10162010	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10467368	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4129745	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4132636	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4132637	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4254189	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4275735	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4277227	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4294679	0.81[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4300508	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4306389	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4312180	0.86[YRI][hapmap]
rs4321067	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4334152	0.81[CHB][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4363738	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4368051	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4432137	0.81[CHB][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4457870	0.80[CHB][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4485233	0.81[CHB][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4492929	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4514547	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4551909	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4556673	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4566029	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4569133	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4586300	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4598779	1.00[ASN][1000 genomes]
rs4606581	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4636783	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4941940	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4943688	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4943689	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4943692	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943693	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6563737	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6563738	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6563739	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6563740	0.80[CHB][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7320424	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7324826	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7325354	0.85[CHB][hapmap];0.81[YRI][hapmap];0.96[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7326555	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326699	0.88[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7327674	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7330016	0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7330515	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74044148	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7991151	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7991758	0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7993726	0.81[CHB][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7993729	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7994665	0.83[CHB][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998582	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7999758	0.81[CHB][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9315723	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9315724	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9532416	0.80[CHB][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532417	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9548872	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9548873	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9548876	0.81[CHB][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9548877	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9548878	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548881	0.96[ASN][1000 genomes]
rs9548883	0.80[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548884	0.81[CHB][hapmap];0.96[ASN][1000 genomes]
rs9548885	0.81[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548895	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9566469	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9594362	0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603589	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9603591	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9603592	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603593	0.86[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9603594	0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9603597	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9603602	0.80[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[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
rs4261404	COG6	cis	Muscle Skeletal	GTEx
rs4261404	COG6	cis	Adipose Subcutaneous	GTEx

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	chr13:40233000-40243200	Weak transcription	Ovary	ovary
45	chr13:40233000-40254600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr13:40233000-40273600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr13:40233000-40295600	Weak transcription	Pancreas	Pancrea
48	chr13:40233200-40253400	Weak transcription	HepG2	liver
49	chr13:40233200-40254600	Weak transcription	Brain Hippocampus Middle	brain
50	chr13:40233400-40243400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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