Variant report

Variant	rs928049
Chromosome Location	chr9:71120013-71120014
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:

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10780985	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1964619	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309312	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs265081	0.95[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs372581	1.00[JPT][hapmap]
rs424970	0.95[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4406476	1.00[JPT][hapmap]
rs4744621	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56320925	0.90[EUR][1000 genomes]
rs6560175	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72716013	0.86[EUR][1000 genomes]
rs7849742	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7854357	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7864227	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902949	0.95[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs928049	RP11-274B18.2	cis	Whole Blood	GTEx
rs928049	PGM5	cis	Whole Blood	GTEx
rs928049	PGM5	cis	cerebellum	SCAN

Chromatin state (count:31 , 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	chr9:71113600-71120200	Strong transcription	Fetal Stomach	stomach
7	chr9:71115200-71120200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr9:71115600-71121400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr9:71116000-71120400	Weak transcription	Aorta	Aorta
10	chr9:71116000-71120600	Weak transcription	Liver	Liver
11	chr9:71116200-71120400	Weak transcription	Psoas Muscle	Psoas
12	chr9:71116200-71124000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr9:71116400-71122000	Weak transcription	HSMMtube	muscle
14	chr9:71116600-71122000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr9:71116800-71120200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr9:71116800-71120800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:71116800-71122000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:71117000-71129600	Weak transcription	NHLF	lung
19	chr9:71117400-71120400	Strong transcription	Fetal Lung	lung
20	chr9:71117400-71122200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr9:71117600-71120200	Weak transcription	Right Ventricle	heart
22	chr9:71117600-71120200	Strong transcription	Stomach Smooth Muscle	stomach
23	chr9:71117600-71120400	Weak transcription	Fetal Heart	heart
24	chr9:71117600-71120600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr9:71117600-71123600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr9:71117600-71142800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr9:71117800-71120200	Weak transcription	Fetal Muscle Leg	muscle
28	chr9:71117800-71120400	Weak transcription	Left Ventricle	heart
29	chr9:71117800-71120400	Weak transcription	Right Atrium	heart
30	chr9:71119200-71122600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr9:71120000-71120800	Genic enhancers	Colon Smooth Muscle	Colon

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