Variant report

Variant	rs9374809
Chromosome Location	chr6:119935496-119935497
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:182573652..182574450-chr6:119934780..119935533,2	MCF-7	breast:
2	chr6:119930273..119931958-chr6:119933352..119935627,2	MCF-7	breast:
3	chr6:119932562..119937060-chr6:119938471..119941600,5	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10782195	0.92[EUR][1000 genomes]
rs11153840	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1572957	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1977147	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2024733	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2024734	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2794256	0.88[CEU][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4245503	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4946434	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7754535	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs807299	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs807309	0.93[EUR][1000 genomes]
rs809889	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs813955	0.87[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9285433	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9320697	0.87[AFR][1000 genomes]
rs9320698	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9372544	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9374810	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9385080	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9398517	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9374809	MAN1A1	cis	cerebellum	SCAN
rs9374809	MAN1A1	cis	parietal	SCAN
rs9374809	PKIB	cis	parietal	SCAN
rs9374809	GPRC6A	cis	cerebellum	SCAN
rs9374809	MAN1A1	cis	lymphoblastoid	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119930600-119948000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr6:119930800-119935600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr6:119932200-119935600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:119932800-119935600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:119933200-119936000	Enhancers	Muscle Satellite Cultured Cells	--
6	chr6:119933200-119936000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:119933200-119942000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:119933400-119935800	Enhancers	HSMM	muscle
9	chr6:119933800-119935800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:119934200-119935600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:119934200-119942400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:119934400-119939600	Weak transcription	HSMMtube	muscle
13	chr6:119934600-119940600	Weak transcription	HMEC	breast
14	chr6:119934800-119942000	Weak transcription	Osteobl	bone
15	chr6:119935200-119935600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:119935200-119935800	Enhancers	H1 Cell Line	embryonic stem cell
17	chr6:119935200-119936000	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr6:119935400-119935600	Enhancers	NHEK	skin
19	chr6:119935400-119935600	Enhancers	NHLF	lung
20	chr6:119935400-119935800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr6:119935400-119936200	Enhancers	HUES48 Cell Line	embryonic stem cell

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