Variant report

Variant	rs11759427
Chromosome Location	chr6:53602109-53602110
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53514929..53516623-chr6:53599837..53602771,2	MCF-7	breast:
2	chr17:56708938..56710691-chr6:53601479..53604353,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11759473	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12662433	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3003498	0.83[GIH][hapmap];0.87[MEX][hapmap]
rs3813850	0.93[CHB][hapmap];0.88[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap]
rs4478409	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4486000	0.83[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs4712042	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715421	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs57853292	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62399939	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6458956	0.80[ASN][1000 genomes]
rs7759593	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9463975	0.94[EUR][1000 genomes]
rs9463976	0.95[EUR][1000 genomes]
rs9474643	0.92[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9474647	0.85[ASW][hapmap];1.00[CEU][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9474650	0.95[EUR][1000 genomes]
rs9474651	0.95[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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11759427	C6orf142	cis	cerebellum	SCAN
rs11759427	RAB23	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53596000-53605600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:53597200-53604000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:53598400-53603000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:53599200-53603000	Enhancers	Fetal Heart	heart
5	chr6:53599400-53602200	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr6:53599400-53602600	Enhancers	HSMMtube	muscle
7	chr6:53599800-53602800	Enhancers	Brain Germinal Matrix	brain
8	chr6:53599800-53603000	Enhancers	HUVEC	blood vessel
9	chr6:53599800-53603200	Enhancers	NHEK	skin
10	chr6:53599800-53606200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:53600000-53605800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:53600800-53603600	Enhancers	Dnd41	blood
13	chr6:53600800-53606200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr6:53601000-53602200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:53601000-53602200	Weak transcription	HMEC	breast
16	chr6:53601000-53602600	Weak transcription	Placenta	Placenta
17	chr6:53601000-53606000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr6:53601000-53606200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr6:53601200-53605800	Weak transcription	Primary T cells from cord blood	blood
20	chr6:53601200-53605800	Weak transcription	Thymus	Thymus
21	chr6:53601200-53606000	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr6:53601200-53606000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:53601200-53606000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr6:53601200-53606000	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr6:53601200-53606200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr6:53601600-53603200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:53601600-53638000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr6:53601800-53602200	Enhancers	Muscle Satellite Cultured Cells	--
29	chr6:53601800-53603000	Enhancers	Hela-S3	cervix
30	chr6:53601800-53603400	Enhancers	Fetal Intestine Large	intestine
31	chr6:53601800-53603400	Enhancers	HepG2	liver
32	chr6:53601800-53603600	Enhancers	Fetal Intestine Small	intestine
33	chr6:53601800-53613400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:53602000-53602200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:53602000-53602200	Enhancers	Duodenum Mucosa	Duodenum
36	chr6:53602000-53602200	Enhancers	Fetal Thymus	thymus
37	chr6:53602000-53602200	Enhancers	NH-A	brain
38	chr6:53602000-53602800	Enhancers	Placenta Amnion	Placenta Amnion
39	chr6:53602000-53603000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:53602000-53603600	Enhancers	Rectal Mucosa Donor 31	rectum

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