Variant report

Variant	rs9469578
Chromosome Location	chr6:33706479-33706480
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33704352..33707039-chr6:33718768..33721610,2	MCF-7	breast:
2	chr6:33706317..33709748-chr6:33710509..33712632,5	MCF-7	breast:
3	chr6:33706241..33709561-chr6:33709640..33714031,4	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1408501	1.00[JPT][hapmap]
rs16869456	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16869458	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16869459	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16869463	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16869464	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16869466	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57303110	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59957785	0.84[EUR][1000 genomes]
rs60447213	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923565	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929527	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6942022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73743323	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73743326	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73743328	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73743329	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73743330	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73743331	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73743333	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73743334	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73743336	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73743398	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73743401	0.84[EUR][1000 genomes]
rs9469580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469581	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9469582	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9469584	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Phosphorus levels	20558539	GWAS catalog

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33686400-33710600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:33690800-33708200	Weak transcription	Gastric	stomach
3	chr6:33691800-33711600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:33692000-33706800	Weak transcription	Fetal Intestine Small	intestine
5	chr6:33692000-33710200	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:33693600-33712000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:33694000-33710600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr6:33695600-33711800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:33699200-33710000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:33699800-33708000	Weak transcription	Fetal Lung	lung
11	chr6:33700200-33706600	Weak transcription	Fetal Intestine Large	intestine
12	chr6:33700400-33707400	Weak transcription	Lung	lung
13	chr6:33700600-33707200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:33702000-33710000	Genic enhancers	HSMM	muscle
15	chr6:33703400-33706800	Weak transcription	Spleen	Spleen
16	chr6:33704400-33707800	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr6:33704600-33706600	Genic enhancers	Brain Substantia Nigra	brain
18	chr6:33704800-33706800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:33704800-33707000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:33705200-33707200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:33705200-33709800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:33705400-33707000	Genic enhancers	Left Ventricle	heart
23	chr6:33705400-33708000	Weak transcription	Brain Anterior Caudate	brain
24	chr6:33705400-33709000	Enhancers	Liver	Liver
25	chr6:33705400-33712000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr6:33705600-33706800	Weak transcription	Right Atrium	heart
27	chr6:33705600-33707600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr6:33705600-33707600	Weak transcription	Placenta	Placenta
29	chr6:33705600-33707600	Weak transcription	HSMMtube	muscle
30	chr6:33705600-33708000	Weak transcription	Brain Angular Gyrus	brain
31	chr6:33705600-33709200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
32	chr6:33705800-33706800	Genic enhancers	Psoas Muscle	Psoas
33	chr6:33705800-33707800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr6:33705800-33711000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:33706000-33706800	Enhancers	Colonic Mucosa	Colon
36	chr6:33706000-33706800	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr6:33706200-33706600	Weak transcription	Brain Hippocampus Middle	brain
38	chr6:33706200-33707000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:33706200-33707400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr6:33706200-33707400	Strong transcription	Fetal Muscle Leg	muscle
41	chr6:33706200-33707800	Genic enhancers	Right Ventricle	heart
42	chr6:33706200-33707800	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
43	chr6:33706400-33706800	Weak transcription	Pancreas	Pancrea
44	chr6:33706400-33708000	Weak transcription	Fetal Heart	heart

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