Variant report

Variant	rs6568788
Chromosome Location	chr6:113736043-113736044
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	chr6:113735341..113737235-chr6:113752412..113754611,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232316	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1009404	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10872098	0.89[ASN][1000 genomes]
rs11153416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883171	0.86[ASN][1000 genomes]
rs2049923	0.89[ASN][1000 genomes]
rs2142639	0.89[ASN][1000 genomes]
rs2348293	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348294	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348295	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348302	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2881870	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4945495	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4945496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568789	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6568790	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568793	0.89[ASN][1000 genomes]
rs6903091	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6903628	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908767	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6915133	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915622	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6926220	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs718459	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718460	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7341217	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7738052	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7739755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768104	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909541	1.00[CHB][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9285411	0.89[ASN][1000 genomes]
rs9320446	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320450	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320459	0.89[ASN][1000 genomes]
rs9374397	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374399	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374401	0.89[ASN][1000 genomes]
rs9387145	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400624	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9481369	0.89[ASN][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	nsv916294	chr6:113518489-113904305	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1034256	chr6:113703567-113793790	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1021815	chr6:113703567-113799956	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6568788	ROS1	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:113726200-113736800	Weak transcription	Colon Smooth Muscle	Colon
2	chr6:113731200-113737200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:113731600-113736200	Enhancers	A549	lung
4	chr6:113733400-113738400	Enhancers	NHDF-Ad	bronchial
5	chr6:113733800-113736200	Enhancers	Osteobl	bone
6	chr6:113733800-113738200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:113733800-113738200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:113734200-113737800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:113735400-113736200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr6:113735400-113736200	Enhancers	NH-A	brain
11	chr6:113735400-113738000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:113735600-113736200	Enhancers	Stomach Smooth Muscle	stomach
13	chr6:113735600-113738200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:113736000-113736200	Enhancers	NHEK	skin
15	chr6:113736000-113736200	Enhancers	NHLF	lung
16	chr6:113736000-113736400	Weak transcription	HSMM	muscle
17	chr6:113736000-113737200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:113736000-113747200	Weak transcription	HMEC	breast

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