Variant report

Variant	rs9491960
Chromosome Location	chr6:128790787-128790788
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12333125	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1417900	0.95[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17053280	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17055907	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35801729	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569535	1.00[CHD][hapmap]
rs6921395	0.86[CEU][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923822	1.00[CHD][hapmap]
rs7751265	1.00[CHD][hapmap]
rs9321120	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9482889	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9491965	0.86[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9491973	1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9491976	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492001	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv830800	chr6:128710631-128878435	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9491960	AKAP7	cis	parietal	SCAN
rs9491960	MOXD1	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128773400-128795200	Weak transcription	HSMMtube	muscle
2	chr6:128780400-128795400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr6:128785600-128794400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:128785600-128795200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:128785600-128795400	Weak transcription	A549	lung
6	chr6:128786200-128792800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr6:128786400-128792800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:128786400-128792800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:128786800-128795600	Weak transcription	HSMM	muscle
10	chr6:128787200-128792800	Weak transcription	Small Intestine	intestine
11	chr6:128787200-128794800	Weak transcription	Right Ventricle	heart
12	chr6:128787200-128795800	Weak transcription	Left Ventricle	heart
13	chr6:128787200-128795800	Weak transcription	Pancreas	Pancrea
14	chr6:128787400-128792800	Weak transcription	Brain Anterior Caudate	brain
15	chr6:128787400-128793200	Weak transcription	Fetal Intestine Large	intestine
16	chr6:128787600-128794800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:128787600-128794800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr6:128787600-128795200	Weak transcription	NHEK	skin
19	chr6:128787600-128799200	Weak transcription	HepG2	liver
20	chr6:128787800-128792800	Weak transcription	Brain Angular Gyrus	brain
21	chr6:128787800-128792800	Weak transcription	Fetal Intestine Small	intestine
22	chr6:128788000-128799000	Weak transcription	Liver	Liver
23	chr6:128788400-128795400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:128788800-128795000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:128790200-128791200	Enhancers	Brain Substantia Nigra	brain
26	chr6:128790400-128791400	Enhancers	Brain Hippocampus Middle	brain
27	chr6:128790600-128790800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr6:128790600-128791200	Enhancers	Fetal Heart	heart
29	chr6:128790600-128796400	Weak transcription	Stomach Mucosa	stomach

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