Variant report

Variant	rs1321081
Chromosome Location	chr6:45355609-45355610
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45344406..45349479-chr6:45352255..45358580,11	MCF-7	breast:
2	chr6:45354546..45357105-chr6:45376893..45379533,2	K562	blood:
3	chr6:45354962..45357015-chr6:45358348..45360567,3	K562	blood:

Variant related genes	Relation type
ENSG00000196284	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10948222	1.00[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10948231	0.89[ASN][1000 genomes]
rs12199720	1.00[CEU][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12205312	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12208924	0.83[CHD][hapmap]
rs12209727	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12525950	0.89[ASN][1000 genomes]
rs12529946	0.84[CHD][hapmap]
rs1285019	0.85[CHD][hapmap]
rs17288334	1.00[ASN][1000 genomes]
rs2396425	0.96[CEU][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap]
rs2396502	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35565233	0.81[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs3749863	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs3923353	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4072928	0.86[CHD][hapmap]
rs4373351	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4446571	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4506035	0.80[EUR][1000 genomes]
rs4510673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400336	1.00[ASN][1000 genomes]
rs6458441	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6901786	0.87[CHD][hapmap]
rs6934594	0.96[CEU][hapmap];0.91[GIH][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6935398	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6937317	0.82[AMR][1000 genomes]
rs717987	0.81[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs7451423	1.00[CEU][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7740083	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7770401	0.88[EUR][1000 genomes]
rs927657	0.83[YRI][hapmap]
rs9296453	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9296457	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9357480	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9357484	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9369552	0.82[EUR][1000 genomes]
rs9369558	1.00[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9381373	0.87[CHD][hapmap]
rs9381383	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9395084	0.92[CEU][hapmap];0.95[TSI][hapmap]
rs9395086	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9395095	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9463076	0.87[CHD][hapmap]
rs9463078	0.83[CEU][hapmap]
rs9463081	0.92[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9463083	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9472451	0.87[CHD][hapmap]
rs9472460	0.81[EUR][1000 genomes]
rs988147	0.87[CHD][hapmap]

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	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1321081	C6orf226	cis	cerebellum	SCAN
rs1321081	SUPT3H	cis	lymphoblastoid	seeQTL
rs1321081	SUPT3H	cis	cerebellum	SCAN
rs1321081	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL
rs1321081	CYP39A1	cis	parietal	SCAN
rs1321081	SUPT3H	cis	parietal	SCAN
rs1321081	CD2AP	cis	parietal	SCAN
rs1321081	MAD2L1BP	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45354200-45356000	Enhancers	Placenta Amnion	Placenta Amnion
2	chr6:45354200-45356200	Enhancers	HSMMtube	muscle
3	chr6:45354200-45357400	Enhancers	HSMM	muscle
4	chr6:45354200-45358600	Enhancers	Muscle Satellite Cultured Cells	--
5	chr6:45354400-45356400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:45354400-45356800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:45354400-45357400	Enhancers	NHDF-Ad	bronchial
8	chr6:45354400-45358200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:45354800-45357400	Enhancers	NHLF	lung
10	chr6:45355000-45356200	Enhancers	Placenta	Placenta
11	chr6:45355000-45356400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:45355000-45356400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:45355200-45356000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:45355200-45357200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:45355600-45356000	Enhancers	Osteobl	bone

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