Variant report

Variant	rs4294679
Chromosome Location	chr13:40292978-40292979
allele	G/T
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:76)

rs_ID	r²[population]
rs10162010	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10467367	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap]
rs10467368	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4129745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4132636	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4132637	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4254189	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4261404	0.81[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4275735	0.93[ASN][1000 genomes]
rs4277227	0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs4300508	0.91[ASN][1000 genomes]
rs4321067	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4334152	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs4363738	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4368051	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4432137	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs4457870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4485233	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs4492929	0.94[ASN][1000 genomes]
rs4514547	0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs4551909	0.92[ASN][1000 genomes]
rs4556673	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4566029	0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs4569133	0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs4586300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4598779	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs4606581	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4636783	0.93[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs4941940	0.94[ASN][1000 genomes]
rs4943688	0.94[ASN][1000 genomes]
rs4943689	0.94[ASN][1000 genomes]
rs4943692	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4943693	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6563737	0.94[ASN][1000 genomes]
rs6563738	0.93[ASN][1000 genomes]
rs6563739	0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs6563740	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7320424	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7324826	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7325354	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7326555	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7326699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7327674	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7330016	0.92[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7330515	0.94[ASN][1000 genomes]
rs74044148	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7991151	0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7991758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7993726	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7993729	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7994665	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7998582	0.93[ASN][1000 genomes]
rs7999758	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs9315723	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9315724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9532416	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9532417	0.94[ASN][1000 genomes]
rs9548872	0.92[ASN][1000 genomes]
rs9548873	0.85[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs9548876	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs9548877	0.94[ASN][1000 genomes]
rs9548878	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548881	0.97[ASN][1000 genomes]
rs9548883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9548885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9566469	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9594362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9603589	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9603591	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9603592	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9603593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9603594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9603597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603602	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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
rs4294679	COG6	cis	Adipose Subcutaneous	GTEx
rs4294679	COG6	cis	Muscle Skeletal	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40233000-40295600	Weak transcription	Pancreas	Pancrea
2	chr13:40246400-40297400	Weak transcription	HUVEC	blood vessel
3	chr13:40255000-40306000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr13:40255800-40340200	Weak transcription	Psoas Muscle	Psoas
5	chr13:40257600-40310800	Weak transcription	Brain Germinal Matrix	brain
6	chr13:40262600-40294000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr13:40262800-40293600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr13:40262800-40311000	Weak transcription	Aorta	Aorta
9	chr13:40262800-40311000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr13:40263000-40297200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr13:40263200-40302600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr13:40263400-40293400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr13:40263400-40293800	Weak transcription	Dnd41	blood
14	chr13:40264600-40293800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr13:40267000-40297400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr13:40267200-40293400	Weak transcription	NHDF-Ad	bronchial
17	chr13:40267200-40296800	Weak transcription	Brain Hippocampus Middle	brain
18	chr13:40267200-40296800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr13:40267200-40297000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr13:40267600-40341200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr13:40269200-40293400	Weak transcription	NH-A	brain
22	chr13:40272000-40294400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr13:40272000-40297400	Weak transcription	Ovary	ovary
24	chr13:40272200-40293400	Weak transcription	Osteobl	bone
25	chr13:40273800-40296200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr13:40274000-40301600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr13:40274400-40293800	Weak transcription	HSMM	muscle
28	chr13:40274600-40327000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr13:40282400-40310800	Weak transcription	Right Ventricle	heart
30	chr13:40283600-40310400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr13:40283600-40311000	Weak transcription	Gastric	stomach
32	chr13:40284000-40298200	Weak transcription	Brain Anterior Caudate	brain
33	chr13:40284200-40310400	Weak transcription	Fetal Stomach	stomach
34	chr13:40284400-40302200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr13:40285200-40317600	Weak transcription	Small Intestine	intestine
36	chr13:40286200-40332200	Weak transcription	Esophagus	oesophagus
37	chr13:40287000-40303000	Weak transcription	NHLF	lung
38	chr13:40287200-40293200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr13:40287200-40295200	Weak transcription	HepG2	liver
40	chr13:40287200-40297600	Weak transcription	Duodenum Mucosa	Duodenum
41	chr13:40287400-40296600	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr13:40287400-40311000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr13:40287400-40311400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr13:40287400-40313000	Weak transcription	NHEK	skin
45	chr13:40287600-40310800	Weak transcription	HSMMtube	muscle
46	chr13:40288000-40294200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr13:40289200-40293400	Weak transcription	Adipose Nuclei	Adipose
48	chr13:40289200-40297400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr13:40289400-40297400	Weak transcription	Fetal Kidney	kidney
50	chr13:40289800-40293000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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