Variant report

Variant	rs6265
Chromosome Location	chr11:27679916-27679917
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10501087	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10767664	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10767665	0.80[CHD][hapmap]
rs11030084	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11030099	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11030100	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11030104	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12419948	0.94[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12575096	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12790234	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12807356	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1488830	0.94[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs16917204	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16917237	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1829469	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2030323	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2049045	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs34379767	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35038967	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35051342	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs36029218	0.83[EUR][1000 genomes]
rs4074134	0.83[EUR][1000 genomes]
rs4244531	0.81[EUR][1000 genomes]
rs4301747	0.84[EUR][1000 genomes]
rs4922793	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4923457	0.83[EUR][1000 genomes]
rs4923460	0.94[CEU][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs4923461	0.94[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs4923463	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4923464	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4923466	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6484312	0.83[CEU][hapmap]
rs6484320	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7103411	0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7103873	0.82[CHB][hapmap]
rs71480157	0.83[EUR][1000 genomes]
rs7483762	0.84[EUR][1000 genomes]
rs7926362	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7934165	0.83[CHD][hapmap]
rs879048	0.82[EUR][1000 genomes]
rs925947	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs988748	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832095	chr11:27538626-27715739	Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

Variant related diseases (count:3)

Disease	PMID	Source
Smoking behavior	20418890	GWAS catalog
Weight	19079260	GWAS catalog
Body mass index	19079260	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6265	IMMP1L	cis	cerebellum	SCAN
rs6265	ANO3	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:27643200-27703600	Weak transcription	Ovary	ovary
2	chr11:27659200-27685200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr11:27667400-27683000	Weak transcription	Gastric	stomach
4	chr11:27668400-27681800	Weak transcription	Psoas Muscle	Psoas
5	chr11:27668600-27685000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:27671400-27681000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr11:27671400-27687200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:27671800-27686200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr11:27672200-27687000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr11:27673000-27704400	Weak transcription	HSMM	muscle
11	chr11:27673400-27687000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:27674400-27681800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr11:27674600-27681600	Weak transcription	NHDF-Ad	bronchial
14	chr11:27675200-27681000	Strong transcription	NH-A	brain
15	chr11:27676600-27681800	Strong transcription	Osteobl	bone
16	chr11:27677400-27680000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:27677400-27680600	Weak transcription	Fetal Intestine Small	intestine
18	chr11:27678000-27684200	Weak transcription	Adipose Nuclei	Adipose
19	chr11:27678200-27680000	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr11:27678200-27684400	Weak transcription	Right Ventricle	heart
21	chr11:27678800-27681400	Strong transcription	A549	lung
22	chr11:27678800-27687000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr11:27679000-27680400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr11:27679000-27684200	Weak transcription	Hela-S3	cervix
25	chr11:27679000-27686400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr11:27679000-27687200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr11:27679000-27693800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr11:27679200-27680000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr11:27679200-27680400	Strong transcription	Left Ventricle	heart
30	chr11:27679200-27681400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr11:27679200-27686600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr11:27679400-27680000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:27679400-27680000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr11:27679400-27680000	Strong transcription	Brain Cingulate Gyrus	brain
35	chr11:27679400-27680000	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr11:27679400-27680200	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr11:27679400-27680200	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr11:27679400-27680200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr11:27679400-27680200	ZNF genes & repeats	Aorta	Aorta
40	chr11:27679400-27680200	Strong transcription	Fetal Stomach	stomach
41	chr11:27679600-27680000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr11:27679600-27680000	ZNF genes & repeats	Pancreas	Pancrea
43	chr11:27679600-27680200	Strong transcription	NHLF	lung
44	chr11:27679600-27682200	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr11:27679800-27680200	Strong transcription	Esophagus	oesophagus
46	chr11:27679800-27680400	Strong transcription	HSMMtube	muscle

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