Variant report

Variant	rs1539613
Chromosome Location	chr9:79416943-79416944
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	chr9:79411398..79414162-chr9:79415943..79417893,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10869818	0.85[ASN][1000 genomes]
rs10869827	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10869833	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10869835	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11145076	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11145080	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11145085	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12353019	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12376845	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1343394	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1936292	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4744812	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7022561	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7046472	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72732653	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7854027	0.85[ASN][1000 genomes]
rs7861202	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7867564	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv2758190	chr9:79365865-79673907	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2759697	chr9:79365865-79673907	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79393600-79423400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr9:79400400-79423600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr9:79400800-79419400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr9:79404000-79419200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr9:79404200-79418400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr9:79404400-79419400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:79405200-79418600	Weak transcription	HSMMtube	muscle
8	chr9:79410400-79423600	Weak transcription	Brain Substantia Nigra	brain
9	chr9:79411600-79421200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr9:79412000-79418600	Weak transcription	Aorta	Aorta
11	chr9:79413400-79431800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr9:79414000-79419000	Weak transcription	Fetal Intestine Small	intestine
13	chr9:79414000-79425600	Weak transcription	Colon Smooth Muscle	Colon
14	chr9:79414000-79432200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr9:79414200-79419400	Weak transcription	HSMM	muscle
16	chr9:79415800-79417200	Weak transcription	Fetal Intestine Large	intestine
17	chr9:79416000-79417200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr9:79416200-79423400	Weak transcription	Brain Hippocampus Middle	brain
19	chr9:79416600-79419000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:79416800-79417000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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