Variant report

Variant	rs4539287
Chromosome Location	chr11:15993057-15993058
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:15987521..15990224-chr11:15992075..15994987,3	K562	blood:
2	chr11:15982733..15985578-chr11:15992590..15995535,2	K562	blood:
3	chr11:15989595..15993069-chr11:16007793..16010685,3	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10734238	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10741687	0.92[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap];0.80[ASN][1000 genomes]
rs10741689	0.81[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs10766291	0.86[TSI][hapmap]
rs10766292	0.86[TSI][hapmap]
rs10766293	0.92[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap]
rs10766294	0.92[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs10766295	0.82[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs10766298	0.82[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs10766300	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs10832538	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10832539	0.87[EUR][1000 genomes]
rs10832540	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10832541	0.92[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10832542	0.92[CEU][hapmap];0.87[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs10832543	0.92[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs10832545	0.80[ASN][1000 genomes]
rs10832551	1.00[YRI][hapmap]
rs10832553	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs10832554	0.82[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs11023806	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11023807	0.87[EUR][1000 genomes]
rs11023808	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11023809	0.87[EUR][1000 genomes]
rs11023810	0.87[EUR][1000 genomes]
rs11023815	0.82[CEU][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs11023819	0.81[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs11023820	0.81[CEU][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap]
rs11023821	0.86[TSI][hapmap]
rs11023823	0.80[ASN][1000 genomes]
rs11023826	0.81[JPT][hapmap]
rs11023833	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs11602209	0.80[ASN][1000 genomes]
rs12276728	0.92[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes]
rs12278364	0.80[ASN][1000 genomes]
rs12418884	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12420343	0.84[EUR][1000 genomes]
rs1455106	0.82[CEU][hapmap];0.91[GIH][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap]
rs35038372	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35189093	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35572903	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs36029390	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3922559	0.86[TSI][hapmap]
rs4237711	0.81[JPT][hapmap]
rs4335501	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs4335502	0.80[JPT][hapmap]
rs4342995	0.86[TSI][hapmap]
rs4437995	0.92[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs4627036	0.87[EUR][1000 genomes]
rs4756841	1.00[ASW][hapmap];0.88[CEU][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4756842	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4757379	0.86[TSI][hapmap]
rs4757380	0.85[CEU][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs9645647	0.85[TSI][hapmap]
rs9645648	0.82[CEU][hapmap];0.92[GIH][hapmap];0.83[TSI][hapmap]

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	nsv832074	chr11:15927105-16100772	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4539287	TMEM86A	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:15990400-15995200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr11:15990400-16011600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:15991200-15993800	Enhancers	Adipose Nuclei	Adipose
4	chr11:15991200-15996000	Weak transcription	Brain Germinal Matrix	brain
5	chr11:15991400-15993200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr11:15991600-15993200	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr11:15991600-15993200	Enhancers	K562	blood
8	chr11:15991600-16006600	Weak transcription	Liver	Liver
9	chr11:15991800-15997200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr11:15991800-15997400	Weak transcription	HepG2	liver
11	chr11:15991800-15998000	Weak transcription	Aorta	Aorta
12	chr11:15991800-16006800	Weak transcription	Fetal Muscle Leg	muscle
13	chr11:15992000-15993200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:15992000-15993600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr11:15992000-15994800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr11:15992000-15997200	Weak transcription	NHLF	lung
17	chr11:15992000-15997400	Weak transcription	Fetal Lung	lung
18	chr11:15992000-15997400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr11:15992200-15993200	Enhancers	Left Ventricle	heart
20	chr11:15992400-15993200	Enhancers	Psoas Muscle	Psoas
21	chr11:15992400-16006600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr11:15992600-15993600	Strong transcription	Fetal Intestine Small	intestine
23	chr11:15992600-15993800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:15992600-15994000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr11:15992600-15997600	Weak transcription	Fetal Heart	heart
26	chr11:15992600-15998000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr11:15992600-16002400	Weak transcription	Stomach Mucosa	stomach
28	chr11:15992600-16006800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:15992800-15997000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:15992800-15997400	Weak transcription	Osteobl	bone
31	chr11:15992800-15998000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr11:15992800-15998000	Weak transcription	NHEK	skin
33	chr11:15993000-15995400	Strong transcription	Fetal Intestine Large	intestine
34	chr11:15993000-15997200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:15993000-15997400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr11:15993000-15999000	Weak transcription	Right Atrium	heart
37	chr11:15993000-16006800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr11:15993000-16010600	Weak transcription	Pancreas	Pancrea
39	chr11:15993000-16012800	Weak transcription	Right Ventricle	heart

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