Variant report

Variant	rs7947059
Chromosome Location	chr11:10268814-10268815
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10500722	0.82[GIH][hapmap]
rs10770100	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10840378	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042682	0.93[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11042685	0.93[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1114426	0.91[AFR][1000 genomes]
rs11607447	0.86[ASN][1000 genomes]
rs12281432	0.92[CHD][hapmap];0.86[ASN][1000 genomes]
rs1372809	0.92[CHD][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1442739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1442740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470260	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17293593	1.00[CEU][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs17294292	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1837978	0.90[AFR][1000 genomes]
rs1988724	0.80[AFR][1000 genomes]
rs2083714	0.93[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2197170	1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2403291	0.90[AFR][1000 genomes]
rs2920150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920152	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4258371	0.93[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4430500	0.86[ASN][1000 genomes]
rs4534577	0.84[AFR][1000 genomes]
rs4550215	0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4553358	0.93[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4612801	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4909923	0.86[ASN][1000 genomes]
rs4910101	0.91[AFR][1000 genomes]
rs4910104	0.93[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4910109	0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4910110	0.84[AFR][1000 genomes]
rs4910111	0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs4910112	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910113	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55879783	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55925664	0.94[EUR][1000 genomes]
rs56035322	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56287081	0.94[EUR][1000 genomes]
rs56352102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57975523	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59033026	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59090117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59807815	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61889814	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67257108	0.86[EUR][1000 genomes]
rs7105045	0.94[EUR][1000 genomes]
rs7110151	0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs7112413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7117478	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7124401	0.86[LWK][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs716804	0.86[ASN][1000 genomes]
rs73419149	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7928530	0.85[EUR][1000 genomes]
rs7935252	0.94[EUR][1000 genomes]
rs7937758	0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7941511	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9804478	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv1039636	chr11:10126747-10280570	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv8789	chr11:10263385-10275029	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7947059	RPL27A	cis	cerebellum	SCAN
rs7947059	TUB	cis	parietal	SCAN
rs7947059	ARFIP2	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10254000-10276200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:10254400-10277400	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr11:10255600-10277200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr11:10255600-10279000	Weak transcription	Small Intestine	intestine
5	chr11:10255800-10277400	Weak transcription	HSMM	muscle
6	chr11:10256000-10270800	Weak transcription	NH-A	brain
7	chr11:10256600-10269600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr11:10257800-10269000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr11:10259200-10280200	Weak transcription	A549	lung
10	chr11:10262400-10271800	Weak transcription	NHDF-Ad	bronchial
11	chr11:10263600-10273400	Weak transcription	Spleen	Spleen
12	chr11:10263600-10280400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:10263800-10280200	Weak transcription	Ovary	ovary
14	chr11:10264600-10277400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr11:10264600-10280400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:10264600-10280800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr11:10264800-10282800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:10266000-10270600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr11:10266600-10272600	Weak transcription	Fetal Stomach	stomach
20	chr11:10266800-10269000	Weak transcription	Aorta	Aorta
21	chr11:10267000-10269600	Weak transcription	Pancreas	Pancrea
22	chr11:10268200-10269000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr11:10268400-10269000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr11:10268400-10269000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr11:10268400-10269000	Enhancers	NHLF	lung
26	chr11:10268400-10269000	Enhancers	Osteobl	bone
27	chr11:10268400-10269600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr11:10268400-10269800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr11:10268600-10269000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:10268600-10269000	Enhancers	Adipose Nuclei	Adipose
31	chr11:10268600-10269200	Weak transcription	Left Ventricle	heart
32	chr11:10268600-10271000	Weak transcription	Fetal Lung	lung
33	chr11:10268600-10276600	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr11:10268600-10300000	Weak transcription	Fetal Intestine Small	intestine
35	chr11:10268800-10269000	Active TSS	Fetal Brain Male	brain
36	chr11:10268800-10274800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr11:10268800-10276600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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