Variant report

Variant	rs9808938
Chromosome Location	chr3:61549568-61549569
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:61547884..61549685-chr3:61773585..61775750,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1574016	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17669146	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1878772	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2886519	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4688636	0.86[CHB][hapmap]
rs6445221	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6445222	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6445224	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7636186	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7640434	0.86[CHB][hapmap]
rs9821236	0.88[ASN][1000 genomes]
rs9824541	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9827952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9840322	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9845678	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv834711	chr3:61413762-61612539	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1008615	chr3:61455419-61679037	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv822105	chr3:61531517-61556259	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	esv1841066	chr3:61534766-61550452	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	esv1837343	chr3:61546425-61550452	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	esv20235	chr3:61546427-61550555	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv590438	chr3:61547707-61549659	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9808938	ABHD6	cis	cerebellum	SCAN
rs9808938	FAM116A	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61545000-61549600	Active TSS	NHEK	skin
2	chr3:61545000-61550800	Active TSS	Psoas Muscle	Psoas
3	chr3:61545400-61549600	Active TSS	Duodenum Mucosa	Duodenum
4	chr3:61545400-61550400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr3:61545400-61550800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr3:61545400-61550800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:61545400-61550800	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr3:61545600-61549600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:61545600-61549600	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr3:61545600-61549800	Active TSS	HSMM	muscle
11	chr3:61545600-61550200	Active TSS	NHLF	lung
12	chr3:61545600-61550600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:61545600-61550600	Active TSS	Colon Smooth Muscle	Colon
14	chr3:61545600-61550600	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr3:61545600-61550600	Active TSS	NHDF-Ad	bronchial
16	chr3:61545600-61550800	Active TSS	H9 Cell Line	embryonic stem cell
17	chr3:61545600-61550800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:61545600-61550800	Active TSS	Fetal Kidney	kidney
19	chr3:61545600-61550800	Active TSS	Left Ventricle	heart
20	chr3:61545600-61550800	Active TSS	HSMMtube	muscle
21	chr3:61545600-61551000	Active TSS	Aorta	Aorta
22	chr3:61545800-61549600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:61545800-61549600	Active TSS	Osteobl	bone
24	chr3:61545800-61549800	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr3:61545800-61549800	Active TSS	Right Ventricle	heart
26	chr3:61545800-61550400	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr3:61545800-61550600	Active TSS	Brain Anterior Caudate	brain
28	chr3:61545800-61550600	Active TSS	Rectal Smooth Muscle	rectum
29	chr3:61545800-61550800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:61545800-61550800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:61545800-61550800	Active TSS	Ovary	ovary
32	chr3:61546000-61549600	Active TSS	Fetal Heart	heart
33	chr3:61546000-61549800	Active TSS	Small Intestine	intestine
34	chr3:61546000-61550200	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr3:61546000-61550400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:61546000-61550600	Active TSS	Lung	lung
37	chr3:61546000-61551000	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr3:61546400-61550600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr3:61547000-61550000	Bivalent/Poised TSS	Fetal Thymus	thymus
40	chr3:61547200-61550200	Bivalent/Poised TSS	Thymus	Thymus
41	chr3:61547400-61549600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:61547600-61551000	Active TSS	Right Atrium	heart
43	chr3:61547800-61550200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
44	chr3:61548000-61550400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
45	chr3:61548200-61550800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
46	chr3:61548400-61549800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr3:61548400-61549800	Flanking Active TSS	Placenta	Placenta
48	chr3:61548400-61550200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
49	chr3:61548400-61550800	Flanking Active TSS	HMEC	breast
50	chr3:61548800-61550400	Active TSS	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links