Variant report

Variant	rs7039076
Chromosome Location	chr9:71115991-71115992
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	chr9:71115432..71117272-chr9:71118792..71122258,3	MCF-7	breast:
2	chr9:71103333..71104874-chr9:71115669..71118300,2	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10868944	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12685375	0.82[JPT][hapmap];0.91[YRI][hapmap]
rs1964621	0.94[ASN][1000 genomes]
rs265080	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36011409	0.84[ASN][1000 genomes]
rs7874438	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs923784	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs923785	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427847	chr9:70318730-71153527	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7039076	PGM5	cis	multi-tissue	Pritchard
rs7039076	MGST2	trans	lymphoblastoid	seeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71102200-71121000	Weak transcription	Fetal Kidney	kidney
2	chr9:71103600-71122000	Weak transcription	Ovary	ovary
3	chr9:71109400-71120600	Weak transcription	Adipose Nuclei	Adipose
4	chr9:71110000-71120600	Weak transcription	Gastric	stomach
5	chr9:71113200-71120600	Weak transcription	Fetal Intestine Large	intestine
6	chr9:71113600-71116200	Strong transcription	Fetal Muscle Trunk	muscle
7	chr9:71113600-71120200	Strong transcription	Fetal Stomach	stomach
8	chr9:71113800-71116000	Strong transcription	Fetal Lung	lung
9	chr9:71114000-71116200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr9:71114200-71116000	Enhancers	Aorta	Aorta
11	chr9:71114200-71116200	Genic enhancers	Left Ventricle	heart
12	chr9:71114200-71116800	Genic enhancers	Colon Smooth Muscle	Colon
13	chr9:71114200-71116800	Enhancers	Right Atrium	heart
14	chr9:71114400-71116000	Weak transcription	Right Ventricle	heart
15	chr9:71114400-71117000	Enhancers	NHLF	lung
16	chr9:71114600-71116600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:71114600-71117600	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr9:71114800-71116400	Enhancers	HSMMtube	muscle
19	chr9:71114800-71116600	Enhancers	NHDF-Ad	bronchial
20	chr9:71114800-71116800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr9:71114800-71117400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr9:71114800-71117600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr9:71115000-71117600	Genic enhancers	Stomach Smooth Muscle	stomach
24	chr9:71115200-71116000	Enhancers	A549	lung
25	chr9:71115200-71116400	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr9:71115200-71116400	Enhancers	HepG2	liver
27	chr9:71115200-71116600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:71115200-71116600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:71115200-71116800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr9:71115200-71116800	Enhancers	Rectal Smooth Muscle	rectum
31	chr9:71115200-71117200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:71115200-71117600	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr9:71115200-71120200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr9:71115400-71116000	Enhancers	Liver	Liver
35	chr9:71115400-71116200	Enhancers	Placenta	Placenta
36	chr9:71115400-71116400	Enhancers	Placenta Amnion	Placenta Amnion
37	chr9:71115400-71116600	Flanking Active TSS	Hela-S3	cervix
38	chr9:71115400-71116800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:71115400-71117600	Enhancers	Fetal Heart	heart
40	chr9:71115600-71116000	Weak transcription	Psoas Muscle	Psoas
41	chr9:71115600-71121400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr9:71115800-71116000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
43	chr9:71115800-71116000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:71115800-71116000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr9:71115800-71116000	Flanking Active TSS	NH-A	brain
46	chr9:71115800-71116400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr9:71115800-71117800	Enhancers	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links