Variant report

Variant	rs4303351
Chromosome Location	chr13:40360754-40360755
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs12584772	0.90[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3012147	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3012153	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3012154	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4603426	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56322803	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6563745	0.90[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6563751	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6650473	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7329513	0.90[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7994943	0.83[JPT][hapmap]
rs9315726	0.81[CHD][hapmap]
rs9532423	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9532427	0.90[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9532435	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548886	0.81[CHD][hapmap]
rs9548899	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9548902	0.90[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9548903	0.90[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9548904	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9548921	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9548923	0.84[ASN][1000 genomes]
rs9548925	0.88[EUR][1000 genomes];0.87[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
rs4303351	COG6	cis	multi-tissue	Pritchard

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40340400-40361200	Weak transcription	Pancreas	Pancrea
2	chr13:40352000-40361400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr13:40354000-40363200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr13:40356400-40360800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr13:40358600-40361200	Weak transcription	Osteobl	bone
6	chr13:40359000-40361000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr13:40359000-40361200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr13:40359000-40361400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr13:40359200-40362800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:40360000-40360800	Flanking Active TSS	HUVEC	blood vessel
11	chr13:40360000-40361600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr13:40360000-40361800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr13:40360000-40361800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr13:40360000-40362800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr13:40360200-40360800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr13:40360200-40360800	Enhancers	Right Atrium	heart
17	chr13:40360200-40361400	Enhancers	Left Ventricle	heart
18	chr13:40360200-40361600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr13:40360200-40361800	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr13:40360200-40361800	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr13:40360200-40362400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr13:40360200-40362600	Enhancers	Fetal Muscle Leg	muscle
23	chr13:40360200-40362800	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr13:40360400-40361400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr13:40360400-40362200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr13:40360400-40362400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr13:40360600-40361000	Weak transcription	Adipose Nuclei	Adipose
28	chr13:40360600-40361000	Weak transcription	Ovary	ovary

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