Variant report

Variant	rs11153838
Chromosome Location	chr6:119911035-119911036
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:119906720..119909415-chr6:119909700..119911588,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11153833	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11962344	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11969898	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12524607	0.88[CEU][hapmap];0.83[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1499564	0.81[EUR][1000 genomes]
rs1603965	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17238430	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17238563	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245503	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4946431	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4946433	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4946434	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56279051	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62418741	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62418744	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62418963	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62418964	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62418966	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62418970	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6902363	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6922474	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72963141	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72963152	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7738144	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7752178	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs807302	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs807303	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9320697	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1027904	chr6:119709488-120001986	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv533518	chr6:119712186-119998618	ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3442553	chr6:119742069-120076777	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1027370	chr6:119869409-120056608	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv538431	chr6:119869409-120056608	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv818452	chr6:119895316-119915332	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11153838	GPRC6A	cis	cerebellum	SCAN
rs11153838	NT5DC1	cis	cerebellum	SCAN
rs11153838	CLVS2	cis	cerebellum	SCAN
rs11153838	WDR69	trans	cerebellum	SCAN
rs11153838	MAN1A1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119908600-119911400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:119909200-119911400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:119909200-119911400	Weak transcription	HMEC	breast
4	chr6:119909400-119911400	Weak transcription	Osteobl	bone
5	chr6:119910800-119912200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr6:119911000-119912000	Enhancers	K562	blood

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