Variant report

Variant	rs2140710
Chromosome Location	chr7:17895575-17895576
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 125 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10249221	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10264355	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10264445	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10264447	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1051603	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11768866	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12699918	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1357796	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1404414	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1404421	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1404422	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1404424	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1404425	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1524774	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1524775	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1524777	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1830006	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1852010	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1852011	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1965534	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1997019	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2030725	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2103144	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2177652	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2254176	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2462512	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2691552	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2691553	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2691555	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2691557	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2691559	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2691581	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2691582	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2691583	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691585	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2691586	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691589	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2691592	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691593	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691594	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2691595	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691596	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691597	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2691600	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2691601	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2691602	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2691604	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691605	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2691607	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2691609	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2691610	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691611	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2691612	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2691613	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2691615	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2691616	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691617	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2691618	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2691620	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2691621	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691623	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2691625	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2691627	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691628	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691629	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691630	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2714875	0.92[EUR][1000 genomes]
rs2714876	0.98[EUR][1000 genomes]
rs2714877	0.98[EUR][1000 genomes]
rs2723494	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2723496	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2723497	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2723498	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2723499	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2723500	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2723501	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2723502	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2723503	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2723504	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2723505	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2723506	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2723507	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2723508	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2723515	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2723540	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2723545	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2723552	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2723553	0.89[EUR][1000 genomes]
rs2723554	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2723555	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2723556	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2723562	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2723567	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2723569	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2723570	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2723571	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2723572	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35819944	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4316058	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4532510	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4543433	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4721661	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4721665	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67452591	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6953831	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6955984	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6958131	0.85[EUR][1000 genomes]
rs6958211	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6973480	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6978097	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6978103	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs949451	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9942602	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs998342	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
4	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
5	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
6	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
7	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
8	nsv830913	chr7:17848480-18034218	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	esv1792752	chr7:17853983-17908546	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1026629	chr7:17862477-18362404	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1025023	chr7:17865796-18357630	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2140710	SNX13	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:17839000-17932600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr7:17841200-17902600	Weak transcription	Brain Anterior Caudate	brain
3	chr7:17846000-17900600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr7:17852600-17896000	Weak transcription	Fetal Kidney	kidney
5	chr7:17852600-17902800	Weak transcription	Colon Smooth Muscle	Colon
6	chr7:17853800-17914000	Weak transcription	Hela-S3	cervix
7	chr7:17854000-17900800	Weak transcription	K562	blood
8	chr7:17876200-17901000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr7:17877600-17902600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:17877800-17917400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr7:17878000-17896000	Weak transcription	Brain Angular Gyrus	brain
12	chr7:17878200-17918400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr7:17879400-17896000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr7:17879400-17896000	Weak transcription	Placenta	Placenta
15	chr7:17879800-17911000	Weak transcription	HepG2	liver
16	chr7:17881000-17897000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr7:17881000-17899000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr7:17881000-17899600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr7:17881000-17901200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr7:17881000-17903400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr7:17881200-17895600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr7:17881400-17903000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr7:17882200-17896400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr7:17884000-17896000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr7:17884600-17907400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr7:17885000-17895600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr7:17885000-17895800	Weak transcription	NHEK	skin
28	chr7:17885000-17928800	Weak transcription	HUVEC	blood vessel
29	chr7:17885200-17933800	Weak transcription	HMEC	breast
30	chr7:17888400-17895600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr7:17888400-17896000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr7:17888400-17896200	Weak transcription	Fetal Stomach	stomach
33	chr7:17888400-17900600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr7:17888400-17900800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr7:17888400-17901000	Weak transcription	NHLF	lung
36	chr7:17888400-17906600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr7:17888400-17934800	Weak transcription	Colonic Mucosa	Colon
38	chr7:17888600-17895600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr7:17888600-17896000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr7:17888600-17896000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr7:17888600-17896000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr7:17888600-17896000	Weak transcription	Fetal Intestine Small	intestine
43	chr7:17888600-17896000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr7:17888600-17896000	Weak transcription	Spleen	Spleen
45	chr7:17888600-17900400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr7:17888600-17900600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr7:17888600-17900600	Weak transcription	Aorta	Aorta
48	chr7:17888600-17900600	Weak transcription	Brain Hippocampus Middle	brain
49	chr7:17888600-17900600	Weak transcription	Pancreas	Pancrea
50	chr7:17888600-17900800	Weak transcription	Lung	lung

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