Variant report

Variant	rs2714857
Chromosome Location	chr7:17958285-17958286
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10216315	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10227224	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10227501	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[ASN][1000 genomes]
rs10227582	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10231926	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10233816	0.96[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs10265373	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10447542	0.96[CEU][hapmap]
rs11768866	0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs11973277	0.96[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11983260	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12699918	0.82[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs12699919	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs1357796	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1404424	0.87[ASN][1000 genomes]
rs1464804	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs1524775	0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs1524776	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1568815	1.00[CEU][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1568817	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1568818	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2103144	0.87[ASN][1000 genomes]
rs2177652	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2691555	0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2691557	0.87[ASN][1000 genomes]
rs2691558	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2691559	0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2691560	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2691561	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2691562	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2691563	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2691564	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2691565	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2691566	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2691567	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2691568	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2691569	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2691570	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2691571	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2691572	0.92[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2691574	0.96[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs2691575	0.83[AFR][1000 genomes]
rs2691576	0.96[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2691577	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2691578	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2691579	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2691580	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2691600	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2691609	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2691611	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2691612	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs2691615	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs2714853	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2714854	0.96[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2714855	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2714856	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2714858	0.96[CEU][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs2714859	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2714860	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2714861	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2714863	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2714864	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2714865	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2714866	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2714867	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2714868	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2714869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2714870	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2714871	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs2714872	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs2714878	1.00[CEU][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2723540	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs35819944	0.85[ASN][1000 genomes]
rs4532510	0.85[ASN][1000 genomes]
rs4543433	0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4719525	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4721670	0.83[AFR][1000 genomes]
rs4721671	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6952907	0.96[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6955984	0.83[ASN][1000 genomes]
rs6962380	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs6973480	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs7802343	0.96[CEU][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap]
rs9942602	0.83[ASN][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
rs2714857	SNX13	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:17911400-17977400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr7:17941400-17958400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr7:17948200-17961000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr7:17948400-17960800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr7:17948600-17962800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr7:17952800-17964400	Weak transcription	Gastric	stomach
7	chr7:17953000-17961600	Weak transcription	Aorta	Aorta
8	chr7:17953000-17963000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr7:17953200-17960600	Weak transcription	Fetal Heart	heart
10	chr7:17953200-17960600	Weak transcription	Right Ventricle	heart
11	chr7:17953200-17964600	Weak transcription	Esophagus	oesophagus
12	chr7:17955000-17977400	Weak transcription	Fetal Intestine Small	intestine
13	chr7:17955200-17960200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr7:17955200-17960600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr7:17955200-17960600	Weak transcription	Left Ventricle	heart
16	chr7:17955200-17964000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:17955200-17966200	Weak transcription	Pancreas	Pancrea
18	chr7:17955400-17960600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr7:17955400-17961200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr7:17955400-17967000	Weak transcription	Lung	lung
21	chr7:17955400-17973000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr7:17956200-17959200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr7:17956800-17958400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr7:17957200-17958400	Enhancers	HepG2	liver
25	chr7:17957800-17960800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr7:17958000-17961800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr7:17958200-17959000	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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