Variant report

Variant	rs13320658
Chromosome Location	chr3:143831886-143831887
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:61879348..61880969-chr3:143831622..143834006,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1354495	0.83[MEX][hapmap]
rs1370029	0.83[MEX][hapmap]
rs1530479	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1583550	0.83[MEX][hapmap]
rs1595211	0.83[MEX][hapmap]
rs2221411	0.83[MEX][hapmap]
rs4431106	0.83[MEX][hapmap]
rs6765491	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6767811	0.83[MEX][hapmap]
rs6775253	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6782558	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6803148	0.83[MEX][hapmap]
rs7631704	0.83[MEX][hapmap]
rs9683376	0.83[MEX][hapmap]
rs9862275	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877568	chr3:143621140-143992630	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3365190	chr3:143642195-143925886	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1010117	chr3:143750590-144093775	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv536748	chr3:143750590-144093775	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1010213	chr3:143775358-143863149	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv591923	chr3:143776096-143862350	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv591924	chr3:143776096-143864780	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1008414	chr3:143779087-143853396	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1009018	chr3:143797683-143868350	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv532633	chr3:143802417-144440646	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv591925	chr3:143821997-144019763	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13320658	HPS3	cis	cerebellum	SCAN
rs13320658	C3orf58	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143825200-143842000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:143828800-143835000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:143829000-143832400	Enhancers	Brain Hippocampus Middle	brain
4	chr3:143829400-143832200	Enhancers	Colon Smooth Muscle	Colon
5	chr3:143829400-143833600	Weak transcription	NHLF	lung
6	chr3:143829600-143834800	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr3:143830000-143833800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:143830000-143847200	Weak transcription	Aorta	Aorta
9	chr3:143830200-143832400	Enhancers	Brain Anterior Caudate	brain
10	chr3:143830800-143832000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:143830800-143832400	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr3:143831000-143832800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:143831000-143832800	Enhancers	Brain Substantia Nigra	brain
14	chr3:143831200-143832200	Weak transcription	Fetal Brain Male	brain
15	chr3:143831200-143833400	Weak transcription	Brain Angular Gyrus	brain
16	chr3:143831400-143832200	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr3:143831600-143833800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:143831600-143837000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:143831600-143838200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:143831600-143838600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:143831800-143832200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:143831800-143833600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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