Variant report

Variant	rs8002731
Chromosome Location	chr13:40362229-40362230
allele	A/C
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	TEAD4	chr13:40362095-40362689	H1-hESC	embryonic stem cell:	n/a	chr13:40362396-40362405
2	MAX	chr13:40362132-40362620	H1-hESC	embryonic stem cell:	n/a	n/a
3	SP1	chr13:40362222-40362545	H1-hESC	embryonic stem cell:	n/a	n/a
4	TEAD4	chr13:40362162-40362583	H1-hESC	embryonic stem cell:	n/a	chr13:40362396-40362405
5	POU5F1	chr13:40362174-40362535	H1-hESC	embryonic stem cell:	n/a	chr13:40362362-40362373
6	E2F6	chr13:40362076-40362689	H1-hESC	embryonic stem cell:	n/a	n/a
7	POU5F1	chr13:40362155-40362555	H1-hESC	embryonic stem cell:	n/a	chr13:40362362-40362373
8	SP1	chr13:40362148-40362507	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr13:40362156-40362604	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
RNY4P14	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11618582	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12872801	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12875311	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12876235	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28635831	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34394770	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7319041	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7320598	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7986796	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7993214	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9532430	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9532433	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9532434	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548932	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9594366	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9603603	0.96[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs9603605	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9603608	1.00[CEU][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9603612	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9603616	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9943	0.92[CEU][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.96[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
rs8002731	COG6	cis	Muscle Skeletal	GTEx

Chromatin state (count:26 , 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	chr13:40360000-40362800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr13:40360200-40362400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr13:40360200-40362600	Enhancers	Fetal Muscle Leg	muscle
6	chr13:40360200-40362800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr13:40360400-40362400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr13:40360800-40362800	Enhancers	HUVEC	blood vessel
9	chr13:40361000-40362400	Enhancers	Ovary	ovary
10	chr13:40361000-40363400	Enhancers	Adipose Nuclei	Adipose
11	chr13:40361200-40362800	Enhancers	HSMMtube	muscle
12	chr13:40361400-40362400	Weak transcription	Left Ventricle	heart
13	chr13:40361400-40362600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr13:40361400-40362600	Enhancers	Fetal Brain Male	brain
15	chr13:40361400-40363600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr13:40361800-40362400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr13:40361800-40362600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr13:40362000-40362600	Enhancers	HSMM	muscle
19	chr13:40362200-40362400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr13:40362200-40362400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr13:40362200-40362600	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr13:40362200-40362600	Enhancers	Fetal Brain Female	brain
23	chr13:40362200-40362800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr13:40362200-40362800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr13:40362200-40362800	Enhancers	H9 Cell Line	embryonic stem cell
26	chr13:40362200-40363600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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