Variant report

Variant	rs9315723
Chromosome Location	chr13:40257949-40257950
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10162010	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10467367	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs10467368	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4129745	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4132636	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4132637	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4254189	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4261404	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4275735	0.99[ASN][1000 genomes]
rs4277227	0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4294679	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]
rs4300508	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4306389	0.83[ASN][1000 genomes]
rs4321067	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4334152	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4363738	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4368051	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4432137	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4457870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4485233	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4492929	1.00[ASN][1000 genomes]
rs4514547	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4551909	0.98[ASN][1000 genomes]
rs4556673	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4566029	0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4569133	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4586300	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4598779	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4606581	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4636783	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4941940	1.00[ASN][1000 genomes]
rs4943688	1.00[ASN][1000 genomes]
rs4943689	1.00[ASN][1000 genomes]
rs4943692	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943693	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6563737	1.00[ASN][1000 genomes]
rs6563738	0.99[ASN][1000 genomes]
rs6563739	0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6563740	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7320424	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7324826	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7325354	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7326555	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7327674	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7330016	0.82[ASW][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7330515	1.00[ASN][1000 genomes]
rs74044148	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7991151	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7991758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7993726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7993729	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7994665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998582	0.99[ASN][1000 genomes]
rs7999758	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9315724	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9532416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532417	1.00[ASN][1000 genomes]
rs9548872	0.98[ASN][1000 genomes]
rs9548873	0.84[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs9548876	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9548877	1.00[ASN][1000 genomes]
rs9548878	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548881	0.96[ASN][1000 genomes]
rs9548883	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548884	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs9548885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9566469	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9594362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603589	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9603591	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9603592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603593	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9603594	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9603597	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9603602	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.91[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9315723	COG6	cis	Adipose Subcutaneous	GTEx
rs9315723	NHLRC3	cis	parietal	SCAN
rs9315723	C13orf36	cis	parietal	SCAN
rs9315723	COG6	cis	Muscle Skeletal	GTEx
rs9315723	COG6	cis	Heart Left Ventricle	GTEx

Chromatin state (count:117 , 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	chr13:40231000-40261800	Weak transcription	Brain Substantia Nigra	brain
6	chr13:40231000-40266200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr13:40231000-40270800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr13:40231000-40286000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr13:40231400-40264200	Weak transcription	Esophagus	oesophagus
10	chr13:40231400-40268000	Weak transcription	Small Intestine	intestine
11	chr13:40231600-40270200	Weak transcription	Gastric	stomach
12	chr13:40233000-40273600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr13:40233000-40295600	Weak transcription	Pancreas	Pancrea
14	chr13:40236800-40261600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr13:40238000-40291600	Weak transcription	Fetal Intestine Small	intestine
16	chr13:40238600-40261600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr13:40241200-40261600	Weak transcription	HSMM	muscle
18	chr13:40246200-40262800	Weak transcription	Fetal Heart	heart
19	chr13:40246400-40297400	Weak transcription	HUVEC	blood vessel
20	chr13:40251200-40258200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr13:40251600-40258400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr13:40252000-40258000	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr13:40252000-40258200	Strong transcription	Fetal Lung	lung
24	chr13:40252200-40258200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr13:40252200-40258200	Strong transcription	Adipose Nuclei	Adipose
26	chr13:40252200-40261800	Weak transcription	K562	blood
27	chr13:40253000-40258200	Strong transcription	NHDF-Ad	bronchial
28	chr13:40253000-40266200	Weak transcription	Colon Smooth Muscle	Colon
29	chr13:40253400-40266600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr13:40254400-40258200	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr13:40254600-40264000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr13:40255000-40258400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr13:40255000-40258600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr13:40255000-40261800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr13:40255000-40261800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr13:40255000-40262400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr13:40255000-40262400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr13:40255000-40262400	Weak transcription	Aorta	Aorta
39	chr13:40255000-40263800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr13:40255000-40264200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr13:40255000-40266600	Weak transcription	Fetal Stomach	stomach
42	chr13:40255000-40268000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr13:40255000-40270000	Weak transcription	Lung	lung
44	chr13:40255000-40291200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr13:40255000-40306000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr13:40255200-40258800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr13:40255200-40261600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr13:40255200-40261800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr13:40255200-40262400	Weak transcription	HSMMtube	muscle
50	chr13:40255200-40265800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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