Variant report

Variant	rs11908227
Chromosome Location	chr20:16244606-16244607
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:16241933..16245769-chr20:16247318..16250085,3	MCF-7	breast:
2	chr20:16243563..16246157-chr20:16249684..16251577,2	K562	blood:
3	chr20:16243563..16246157-chr20:16249683..16251577,3	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10485549	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10485550	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11907241	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11908242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16997595	1.00[JPT][hapmap]
rs17730901	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17731020	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3848791	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4052895	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41276366	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4287828	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4416282	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4814466	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4814467	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6105560	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6105564	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs6110998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6110999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6111001	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6111004	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6111005	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6111007	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6111008	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6111012	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6111025	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs718610	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs878582	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs878583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv833930	chr20:16134347-16302763	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv519621	chr20:16236837-16248453	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv516591	chr20:16238023-16248453	ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11908227	LOC100130264	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16240600-16246200	Weak transcription	Gastric	stomach
2	chr20:16242000-16244800	Enhancers	Ovary	ovary
3	chr20:16242400-16275000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr20:16242800-16245400	Enhancers	Fetal Muscle Leg	muscle
5	chr20:16242800-16245600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr20:16243400-16244800	Enhancers	Spleen	Spleen
7	chr20:16243800-16244800	Enhancers	Fetal Brain Female	brain
8	chr20:16244000-16244800	Enhancers	Fetal Muscle Trunk	muscle
9	chr20:16244000-16244800	Enhancers	Lung	lung
10	chr20:16244000-16245000	Enhancers	Fetal Brain Male	brain
11	chr20:16244400-16244800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr20:16244600-16244800	Enhancers	Brain Inferior Temporal Lobe	brain

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