Variant report

Variant	rs9532435
Chromosome Location	chr13:40361611-40361612
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr13:40361473-40361614	HepG2	liver:	n/a	n/a
2	EP300	chr13:40360898-40361662	SK-N-SH_RA	brain:	n/a	n/a
3	EP300	chr13:40360817-40361669	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
RNY4P14	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12584772	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3012147	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3012153	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3012154	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4603426	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56322803	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6563745	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6563751	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6650473	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7329513	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9532423	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9532427	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9548899	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9548902	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9548903	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9548904	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9548921	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9548923	0.83[ASN][1000 genomes]
rs9548925	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][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
rs9532435	COG6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40354000-40363200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:40359200-40362800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:40360000-40361800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:40360000-40361800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr13:40360000-40362800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr13:40360200-40361800	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr13:40360200-40361800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr13:40360200-40362400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr13:40360200-40362600	Enhancers	Fetal Muscle Leg	muscle
10	chr13:40360200-40362800	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr13:40360400-40362200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr13:40360400-40362400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr13:40360800-40362800	Enhancers	HUVEC	blood vessel
14	chr13:40361000-40361800	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr13:40361000-40362400	Enhancers	Ovary	ovary
16	chr13:40361000-40363400	Enhancers	Adipose Nuclei	Adipose
17	chr13:40361200-40361800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr13:40361200-40361800	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr13:40361200-40362800	Enhancers	HSMMtube	muscle
20	chr13:40361400-40362000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr13:40361400-40362000	Weak transcription	HSMM	muscle
22	chr13:40361400-40362400	Weak transcription	Left Ventricle	heart
23	chr13:40361400-40362600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr13:40361400-40362600	Enhancers	Fetal Brain Male	brain
25	chr13:40361400-40363600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr13:40361600-40362200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr13:40361600-40362200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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