Variant report

Variant	rs2723562
Chromosome Location	chr7:17846620-17846621
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 124 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10249221	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10264355	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10264445	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10264447	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1051603	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11768866	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12699918	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1357796	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1404414	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1404421	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1404422	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1404424	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1404425	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1524774	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1524775	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1524777	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1830006	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1852010	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1852011	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1965534	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1997019	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2030725	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2103144	0.90[EUR][1000 genomes]
rs2140710	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2177652	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2254176	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2462512	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2691552	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2691553	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2691555	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2691557	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2691559	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2691581	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2691582	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2691583	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2691584	0.83[AFR][1000 genomes]
rs2691585	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2691586	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2691589	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2691592	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2691593	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2691594	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2691595	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2691596	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2691597	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2691600	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2691601	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2691602	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2691604	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2691605	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2691607	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2691609	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2691610	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2691611	0.94[EUR][1000 genomes]
rs2691612	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2691613	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2691615	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2691616	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2691617	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2691618	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2691620	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2691621	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2691623	0.86[EUR][1000 genomes]
rs2691625	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2691627	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2691628	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2691629	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2691630	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2714875	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2714876	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2714877	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2723494	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2723496	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2723497	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2723498	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2723499	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2723500	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2723501	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2723502	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2723503	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2723504	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2723505	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2723506	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2723507	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2723508	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2723515	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2723540	0.92[EUR][1000 genomes]
rs2723545	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2723552	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2723553	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2723554	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2723555	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2723556	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2723567	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2723569	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2723570	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2723571	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2723572	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35819944	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4316058	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4532510	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4543433	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4721661	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4721665	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67452591	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6953831	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6955984	0.81[EUR][1000 genomes]
rs6958131	0.92[EUR][1000 genomes]
rs6958211	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6973480	0.81[EUR][1000 genomes]
rs6978097	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6978103	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs949451	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs998342	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869352	chr7:17237983-17932878	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1021524	chr7:17251148-17963307	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1021289	chr7:17254117-17873816	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv538754	chr7:17254117-17873816	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv534309	chr7:17254118-17932878	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv533938	chr7:17254118-18040301	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv887804	chr7:17571140-17885468	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1024398	chr7:17630148-18545073	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
9	nsv538764	chr7:17630148-18545073	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
10	esv1802979	chr7:17816528-17908546	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2723562	SNX13	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:17812400-17852200	Weak transcription	Esophagus	oesophagus
2	chr7:17812600-17887600	Weak transcription	Gastric	stomach
3	chr7:17813600-17879200	Weak transcription	HSMMtube	muscle
4	chr7:17817400-17887600	Weak transcription	Pancreas	Pancrea
5	chr7:17821800-17847000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr7:17822000-17852600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr7:17823200-17854400	Weak transcription	Lung	lung
8	chr7:17823600-17887600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr7:17824800-17861800	Weak transcription	Fetal Heart	heart
10	chr7:17825800-17887600	Weak transcription	Colonic Mucosa	Colon
11	chr7:17826000-17847000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:17826400-17852400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:17826400-17853200	Weak transcription	Aorta	Aorta
14	chr7:17826400-17864000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:17827400-17877600	Weak transcription	Small Intestine	intestine
16	chr7:17828800-17847800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr7:17832000-17849000	Weak transcription	Fetal Brain Female	brain
18	chr7:17832000-17862600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr7:17832000-17880600	Weak transcription	GM12878-XiMat	blood
20	chr7:17834000-17852400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr7:17834000-17853000	Weak transcription	Hela-S3	cervix
22	chr7:17834000-17887800	Weak transcription	Right Ventricle	heart
23	chr7:17834200-17879400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr7:17834400-17852200	Weak transcription	Brain Germinal Matrix	brain
25	chr7:17834800-17888800	Weak transcription	Brain Substantia Nigra	brain
26	chr7:17837600-17846800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr7:17837800-17852000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr7:17837800-17855400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr7:17838000-17852200	Weak transcription	Brain Hippocampus Middle	brain
30	chr7:17838800-17887600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr7:17839000-17847000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr7:17839000-17932600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr7:17839200-17852200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr7:17841000-17847000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr7:17841000-17861000	Weak transcription	NHDF-Ad	bronchial
36	chr7:17841000-17862000	Weak transcription	HUVEC	blood vessel
37	chr7:17841200-17851600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr7:17841200-17883800	Weak transcription	HMEC	breast
39	chr7:17841200-17902600	Weak transcription	Brain Anterior Caudate	brain
40	chr7:17841400-17852400	Weak transcription	Colon Smooth Muscle	Colon
41	chr7:17841400-17862200	Weak transcription	NH-A	brain
42	chr7:17841400-17862200	Weak transcription	NHEK	skin
43	chr7:17841400-17862800	Weak transcription	Stomach Mucosa	stomach
44	chr7:17841600-17879400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr7:17841800-17847200	Weak transcription	Fetal Muscle Leg	muscle
46	chr7:17841800-17849000	Weak transcription	HepG2	liver
47	chr7:17841800-17852000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr7:17842000-17852000	Weak transcription	Left Ventricle	heart
49	chr7:17842000-17853200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr7:17842400-17853000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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