Variant report

Variant	rs521546
Chromosome Location	chr9:18709330-18709331
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:18705469..18707872-chr9:18709248..18712015,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178031	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10811021	0.84[ASN][1000 genomes]
rs2507117	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs2570568	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2779124	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2779127	0.81[ASW][hapmap]
rs479642	0.89[ASN][1000 genomes]
rs480335	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs482009	0.93[CHD][hapmap];0.85[MEX][hapmap];0.86[ASN][1000 genomes]
rs484122	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs487882	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs502981	0.82[AMR][1000 genomes]
rs507556	0.92[AMR][1000 genomes]
rs518607	1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519115	0.84[AMR][1000 genomes]
rs519878	0.84[AMR][1000 genomes]
rs521911	0.93[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs530120	0.94[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.90[ASN][1000 genomes]
rs531847	0.84[AMR][1000 genomes]
rs532101	0.94[ASN][1000 genomes]
rs542826	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs542956	0.84[AMR][1000 genomes]
rs563805	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs574090	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs574151	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs580568	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs776569	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1029449	chr9:18414752-18829127	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv540077	chr9:18414752-18829127	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv1030931	chr9:18414752-18903530	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv892691	chr9:18519699-18805483	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv892692	chr9:18519699-19045502	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv831523	chr9:18592398-18753451	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	nsv892694	chr9:18599029-18767830	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
11	nsv613726	chr9:18676163-18709330	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
12	nsv892697	chr9:18700566-18767830	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs521546	MYL3	trans	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18675800-18710000	Strong transcription	HSMM	muscle
2	chr9:18690000-18714200	Weak transcription	HUVEC	blood vessel
3	chr9:18704400-18710600	Genic enhancers	NHDF-Ad	bronchial
4	chr9:18705800-18711200	Strong transcription	Muscle Satellite Cultured Cells	--
5	chr9:18706200-18721200	Weak transcription	Aorta	Aorta
6	chr9:18707200-18710000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr9:18707200-18720800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:18707600-18709800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:18707600-18709800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:18707600-18709800	Weak transcription	HSMMtube	muscle
11	chr9:18707600-18710000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:18707600-18711200	Enhancers	Fetal Heart	heart
13	chr9:18707800-18710000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:18708000-18711000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:18708000-18722400	Weak transcription	NHLF	lung
16	chr9:18708200-18709800	Weak transcription	Adipose Nuclei	Adipose
17	chr9:18708200-18709800	Weak transcription	NH-A	brain
18	chr9:18708600-18709600	Strong transcription	Osteobl	bone
19	chr9:18708600-18709800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:18708600-18718400	Weak transcription	Fetal Stomach	stomach
21	chr9:18708600-18726400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr9:18708800-18709600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:18708800-18721400	Weak transcription	Fetal Lung	lung
24	chr9:18708800-18727000	Weak transcription	Stomach Smooth Muscle	stomach

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