Variant report

Variant	rs2691579
Chromosome Location	chr7:17956523-17956524
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10216315	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10227224	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10227501	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10227582	0.90[ASN][1000 genomes]
rs10231926	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10233816	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs10265373	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10447542	0.96[EUR][1000 genomes]
rs11768866	0.80[ASN][1000 genomes]
rs11973277	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11983260	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12699918	0.82[ASN][1000 genomes]
rs12699919	0.96[EUR][1000 genomes]
rs1404424	0.83[ASN][1000 genomes]
rs1464804	0.81[ASN][1000 genomes]
rs1524775	0.83[ASN][1000 genomes]
rs1568815	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1568817	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1568818	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2103144	0.84[ASN][1000 genomes]
rs2691555	0.82[ASN][1000 genomes]
rs2691557	0.83[ASN][1000 genomes]
rs2691558	0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2691559	0.83[ASN][1000 genomes]
rs2691560	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2691561	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2691562	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2691563	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2691564	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2691565	0.81[ASN][1000 genomes]
rs2691566	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2691567	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2691568	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2691569	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2691570	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2691571	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2691572	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2691573	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2691575	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2691576	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2691577	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2691578	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2691580	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2714853	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2714854	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2714855	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2714856	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2714857	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2714858	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2714859	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2714860	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2714861	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2714863	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2714864	0.93[ASN][1000 genomes]
rs2714865	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2714866	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2714867	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2714868	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2714869	0.92[ASN][1000 genomes]
rs2714870	0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2714872	0.82[ASN][1000 genomes]
rs2714878	0.81[AFR][1000 genomes]
rs35819944	0.81[ASN][1000 genomes]
rs4532510	0.82[ASN][1000 genomes]
rs4543433	0.80[ASN][1000 genomes]
rs4719525	0.89[ASN][1000 genomes]
rs4721670	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4721671	0.88[ASN][1000 genomes]
rs6952907	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6962380	0.96[EUR][1000 genomes]
rs7802343	0.83[AFR][1000 genomes];0.97[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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv1030201	chr7:17898410-18491985	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
9	nsv887808	chr7:17920613-18150005	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1018517	chr7:17926468-18127372	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv606357	chr7:17938491-18375245	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	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
rs2691579	SNX13	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:17900400-17956600	Weak transcription	A549	lung
2	chr7:17911400-17977400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr7:17941400-17958400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:17947400-17956600	Weak transcription	Fetal Lung	lung
5	chr7:17947400-17957400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr7:17948200-17961000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr7:17948400-17960800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr7:17948600-17962800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr7:17950800-17956800	Weak transcription	Primary B cells from cord blood	blood
10	chr7:17951600-17956600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr7:17952800-17964400	Weak transcription	Gastric	stomach
12	chr7:17953000-17961600	Weak transcription	Aorta	Aorta
13	chr7:17953000-17963000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr7:17953200-17960600	Weak transcription	Fetal Heart	heart
15	chr7:17953200-17960600	Weak transcription	Right Ventricle	heart
16	chr7:17953200-17964600	Weak transcription	Esophagus	oesophagus
17	chr7:17954600-17957600	Weak transcription	Liver	Liver
18	chr7:17955000-17977400	Weak transcription	Fetal Intestine Small	intestine
19	chr7:17955200-17960200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr7:17955200-17960600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:17955200-17960600	Weak transcription	Left Ventricle	heart
22	chr7:17955200-17964000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr7:17955200-17966200	Weak transcription	Pancreas	Pancrea
24	chr7:17955400-17957200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr7:17955400-17960600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr7:17955400-17961200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr7:17955400-17967000	Weak transcription	Lung	lung
28	chr7:17955400-17973000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr7:17955600-17957200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr7:17956000-17956800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr7:17956200-17956600	Weak transcription	HepG2	liver
32	chr7:17956200-17959200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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