Variant report

Variant	rs9532434
Chromosome Location	chr13:40355913-40355914
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	chr13:40355682..40357297-chr13:41239680..41242303,2	MCF-7	breast:
2	chr13:40355345..40357522-chr13:41236727..41239020,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150907	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11618582	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12872801	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12875311	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12876235	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17591266	0.83[AFR][1000 genomes]
rs28635831	0.99[EUR][1000 genomes]
rs34394770	0.99[EUR][1000 genomes]
rs7319041	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7320598	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7986796	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7993214	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8002731	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532430	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9532432	0.80[AFR][1000 genomes]
rs9532433	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548932	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9594366	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9603603	0.88[EUR][1000 genomes]
rs9603605	0.96[EUR][1000 genomes]
rs9603608	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9603612	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9603616	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9943	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1054797	chr13:40198744-40618428	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking 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	10 gene(s)	inside rSNPs	diseases
3	nsv541755	chr13:40198744-40618428	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv832586	chr13:40222880-40379063	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1040458	chr13:40249387-40638129	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9532434	COG6	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40340400-40361200	Weak transcription	Pancreas	Pancrea
2	chr13:40341800-40356600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr13:40342600-40360200	Weak transcription	Fetal Muscle Leg	muscle
4	chr13:40350200-40357200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr13:40351800-40358400	Weak transcription	Ovary	ovary
6	chr13:40351800-40360200	Weak transcription	Left Ventricle	heart
7	chr13:40352000-40361400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr13:40353400-40357000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr13:40353800-40358000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr13:40353800-40358400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr13:40353800-40360000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr13:40354000-40358200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr13:40354000-40358800	Weak transcription	NHLF	lung
14	chr13:40354000-40363200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr13:40354400-40358200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr13:40354400-40358400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr13:40354600-40358200	Weak transcription	Osteobl	bone
18	chr13:40354600-40360200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr13:40355000-40356000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr13:40355000-40356600	Enhancers	Brain Substantia Nigra	brain
21	chr13:40355200-40356400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr13:40355200-40357400	Weak transcription	HUVEC	blood vessel
23	chr13:40355400-40358200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr13:40355600-40356000	Weak transcription	Brain Cingulate Gyrus	brain

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