Variant report

Variant	rs599947
Chromosome Location	chr11:57013248-57013249
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57011184..57013387-chr11:57014609..57016452,2	K562	blood:
2	chr11:56894402..56895909-chr11:57012164..57014326,2	K562	blood:
3	chr11:56923234..56925283-chr11:57012223..57015017,2	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10736682	0.81[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10792079	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10792083	0.81[JPT][hapmap]
rs10896595	0.87[ASN][1000 genomes]
rs10896597	0.95[ASN][1000 genomes]
rs10896599	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11228968	0.89[ASN][1000 genomes]
rs11228975	0.89[ASN][1000 genomes]
rs11228976	0.89[ASN][1000 genomes]
rs11228978	0.89[ASN][1000 genomes]
rs11228980	0.89[ASN][1000 genomes]
rs11228982	0.83[ASN][1000 genomes]
rs11228984	0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs11228985	0.87[ASN][1000 genomes]
rs11602501	0.86[TSI][hapmap]
rs11604560	0.89[ASN][1000 genomes]
rs11605053	0.87[ASN][1000 genomes]
rs11607817	0.89[ASN][1000 genomes]
rs12419065	0.81[ASN][1000 genomes]
rs12421633	0.89[ASN][1000 genomes]
rs12421755	0.89[ASN][1000 genomes]
rs12792781	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12797769	0.88[ASN][1000 genomes]
rs17572970	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17573746	0.84[TSI][hapmap]
rs17651610	0.89[ASN][1000 genomes]
rs17652078	0.89[ASN][1000 genomes]
rs1892963	0.89[ASN][1000 genomes]
rs1892964	0.95[ASN][1000 genomes]
rs1893675	0.82[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1939489	0.87[ASN][1000 genomes]
rs1939495	0.89[ASN][1000 genomes]
rs2155230	0.89[ASN][1000 genomes]
rs2155231	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2226613	0.86[ASN][1000 genomes]
rs2276038	0.82[JPT][hapmap]
rs2511026	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2511029	1.00[ASN][1000 genomes]
rs2511030	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2846042	0.95[ASN][1000 genomes]
rs2846049	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2846050	0.95[ASN][1000 genomes]
rs2846051	0.98[ASN][1000 genomes]
rs2851722	0.95[ASN][1000 genomes]
rs35610294	0.88[ASN][1000 genomes]
rs3935068	0.85[ASN][1000 genomes]
rs4384399	0.89[ASN][1000 genomes]
rs4565915	0.87[ASN][1000 genomes]
rs479949	0.95[ASN][1000 genomes]
rs4938855	0.89[ASN][1000 genomes]
rs4938857	0.89[ASN][1000 genomes]
rs4938859	0.88[ASN][1000 genomes]
rs4938861	0.84[ASN][1000 genomes]
rs4939132	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs499318	0.95[ASN][1000 genomes]
rs5012051	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.96[ASN][1000 genomes]
rs519277	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs522656	1.00[ASN][1000 genomes]
rs528101	0.95[ASN][1000 genomes]
rs58295319	0.81[ASN][1000 genomes]
rs590240	1.00[ASN][1000 genomes]
rs625565	0.95[ASN][1000 genomes]
rs652016	0.92[ASN][1000 genomes]
rs654635	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6591413	0.89[ASN][1000 genomes]
rs6591415	0.89[ASN][1000 genomes]
rs6591416	0.87[ASN][1000 genomes]
rs6591417	0.87[ASN][1000 genomes]
rs7102963	0.89[ASN][1000 genomes]
rs7120644	0.89[ASN][1000 genomes]
rs7128371	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7130020	0.80[TSI][hapmap]
rs7130252	0.89[ASN][1000 genomes]
rs72921992	0.86[ASN][1000 genomes]
rs7928905	0.90[EUR][1000 genomes]
rs7935236	0.83[ASN][1000 genomes]
rs948844	0.82[ASW][hapmap];0.82[CEU][hapmap];0.94[GIH][hapmap];0.98[LWK][hapmap];0.96[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs948847	0.89[GIH][hapmap];0.83[TSI][hapmap]
rs9943582	0.82[CEU][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915640	chr11:56814841-57139786	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv482317	chr11:56857026-57028631	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs599947	OR4C6	cis	parietal	SCAN
rs599947	SLC43A3	cis	cerebellum	SCAN
rs599947	MS4A3	cis	cerebellum	SCAN
rs599947	OR5M9	cis	cerebellum	SCAN
rs599947	GLYATL2	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57005200-57016400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr11:57008800-57016200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr11:57009600-57016600	Weak transcription	Liver	Liver
4	chr11:57009800-57016400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr11:57010000-57016400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:57011000-57015000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:57012000-57013400	Enhancers	Spleen	Spleen
8	chr11:57012400-57016400	Weak transcription	K562	blood
9	chr11:57013000-57016200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr11:57013000-57017600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr11:57013200-57013600	Weak transcription	Placenta	Placenta
12	chr11:57013200-57016200	Weak transcription	Adipose Nuclei	Adipose
13	chr11:57013200-57016200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr11:57013200-57016400	Weak transcription	Fetal Muscle Leg	muscle
15	chr11:57013200-57016400	Weak transcription	Left Ventricle	heart
16	chr11:57013200-57016400	Weak transcription	Lung	lung
17	chr11:57013200-57016800	Weak transcription	HUVEC	blood vessel

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