Variant report

Variant	rs2691629
Chromosome Location	chr7:17824631-17824632
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	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10264355	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10264445	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10264447	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1051603	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11768866	0.89[EUR][1000 genomes]
rs12699918	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1357796	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1404414	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1404421	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1404422	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1404424	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1404425	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1524774	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1524775	0.90[EUR][1000 genomes]
rs1524777	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1830006	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1852010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1852011	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1965534	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1997019	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2030725	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2103144	0.89[EUR][1000 genomes]
rs2140710	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2177652	0.80[EUR][1000 genomes]
rs2254176	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2462512	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2691552	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2691555	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2691556	0.80[AFR][1000 genomes]
rs2691557	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2691559	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2691581	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2691582	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2691583	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2691585	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2691586	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2691589	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2691592	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2691593	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2691594	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2691595	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2691596	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2691597	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2691600	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2691601	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2691602	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2691604	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2691605	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2691607	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2691609	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2691610	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2691611	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2691612	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2691613	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2691615	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2691616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2691617	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2691618	0.92[EUR][1000 genomes]
rs2691620	0.92[EUR][1000 genomes]
rs2691621	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2691623	0.85[EUR][1000 genomes]
rs2691625	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2691627	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2691628	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2691630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2714875	0.84[EUR][1000 genomes]
rs2714876	0.91[EUR][1000 genomes]
rs2714877	0.91[EUR][1000 genomes]
rs2723494	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2723496	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2723497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2723498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2723499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2723500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2723501	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2723502	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2723503	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2723504	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2723505	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2723506	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2723507	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2723508	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2723510	0.80[AFR][1000 genomes]
rs2723511	0.80[AFR][1000 genomes]
rs2723515	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2723540	0.91[EUR][1000 genomes]
rs2723545	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2723552	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2723553	0.95[EUR][1000 genomes]
rs2723554	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2723555	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2723556	0.95[EUR][1000 genomes]
rs2723562	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2723567	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2723569	0.92[EUR][1000 genomes]
rs2723570	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2723571	0.92[EUR][1000 genomes]
rs2723572	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35819944	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4316058	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4532510	0.88[EUR][1000 genomes]
rs4543433	0.89[EUR][1000 genomes]
rs4721661	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4721665	0.90[EUR][1000 genomes]
rs67452591	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6953831	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6958131	0.91[EUR][1000 genomes]
rs6958211	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6978097	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6978103	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs949451	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs998342	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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
rs2691629	SNX13	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:17812400-17846200	Weak transcription	Fetal Stomach	stomach
2	chr7:17812400-17852200	Weak transcription	Esophagus	oesophagus
3	chr7:17812600-17887600	Weak transcription	Gastric	stomach
4	chr7:17813600-17879200	Weak transcription	HSMMtube	muscle
5	chr7:17813800-17833200	Weak transcription	Fetal Thymus	thymus
6	chr7:17813800-17836200	Weak transcription	HSMM	muscle
7	chr7:17814200-17833200	Weak transcription	Right Ventricle	heart
8	chr7:17814600-17828600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:17814600-17833400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr7:17815000-17833200	Weak transcription	Left Ventricle	heart
11	chr7:17815200-17829200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr7:17816200-17833200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:17817400-17887600	Weak transcription	Pancreas	Pancrea
14	chr7:17820800-17833200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr7:17821200-17827000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr7:17821800-17833200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr7:17821800-17847000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:17822000-17846200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr7:17822000-17852600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr7:17822200-17837000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr7:17822200-17845600	Weak transcription	NHLF	lung
22	chr7:17822400-17826800	Weak transcription	Thymus	Thymus
23	chr7:17822400-17833000	Weak transcription	Osteobl	bone
24	chr7:17822400-17833200	Weak transcription	Fetal Muscle Leg	muscle
25	chr7:17822600-17832800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr7:17822600-17833200	Weak transcription	HUVEC	blood vessel
27	chr7:17822600-17833200	Weak transcription	NH-A	brain
28	chr7:17823000-17846200	Weak transcription	Fetal Intestine Small	intestine
29	chr7:17823200-17854400	Weak transcription	Lung	lung
30	chr7:17823400-17833000	Weak transcription	Primary T cells from cord blood	blood
31	chr7:17823600-17887600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr7:17823800-17833000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr7:17823800-17833200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr7:17824000-17833200	Weak transcription	HMEC	breast
35	chr7:17824000-17841000	Weak transcription	NHEK	skin
36	chr7:17824600-17824800	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links