Variant report

Variant	rs7824298
Chromosome Location	chr8:69142887-69142888
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1058194	0.83[EUR][1000 genomes]
rs10957423	0.87[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10957424	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10957425	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12541905	0.83[EUR][1000 genomes]
rs12544661	0.83[EUR][1000 genomes]
rs12546271	0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs12547567	0.83[EUR][1000 genomes]
rs12547594	0.83[EUR][1000 genomes]
rs12548558	0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs12549883	0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs12549980	0.83[EUR][1000 genomes]
rs12549988	0.83[EUR][1000 genomes]
rs12681348	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13257592	0.83[EUR][1000 genomes]
rs13258486	0.83[EUR][1000 genomes]
rs13262547	0.81[EUR][1000 genomes]
rs13271545	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13271692	0.83[EUR][1000 genomes]
rs13272579	0.83[EUR][1000 genomes]
rs13281136	0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs13282050	0.83[EUR][1000 genomes]
rs1404600	0.83[EUR][1000 genomes]
rs1404601	0.83[EUR][1000 genomes]
rs1525054	0.83[EUR][1000 genomes]
rs1525055	0.83[EUR][1000 genomes]
rs1525056	0.83[EUR][1000 genomes]
rs16934405	0.81[EUR][1000 genomes]
rs17450699	0.81[CHB][hapmap]
rs1880538	0.83[EUR][1000 genomes]
rs1917544	0.83[EUR][1000 genomes]
rs2280636	0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs2280637	0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs2280638	0.83[EUR][1000 genomes]
rs2280639	0.83[EUR][1000 genomes]
rs2280640	0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs2280641	0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs35741702	0.83[EUR][1000 genomes]
rs6472391	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6472392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6984731	0.83[EUR][1000 genomes]
rs7004629	0.82[EUR][1000 genomes]
rs7005736	0.84[EUR][1000 genomes]
rs7819467	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs940664	0.83[EUR][1000 genomes]
rs940665	0.87[TSI][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3331644	chr8:68806705-69189171	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1028889	chr8:69026806-69308725	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv948687	chr8:69041121-69642540	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv890976	chr8:69100070-69155563	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7824298	MSC	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:69130000-69151800	Weak transcription	Lung	lung
2	chr8:69130800-69143600	Weak transcription	HUVEC	blood vessel
3	chr8:69131000-69151200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr8:69131200-69145000	Weak transcription	Fetal Stomach	stomach
5	chr8:69133000-69151800	Weak transcription	Left Ventricle	heart
6	chr8:69140000-69143000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr8:69140000-69143800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr8:69141200-69143000	Enhancers	H1 Cell Line	embryonic stem cell
9	chr8:69141200-69143000	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr8:69141200-69143000	Enhancers	NHDF-Ad	bronchial
11	chr8:69141200-69143200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr8:69141200-69143200	Enhancers	Adipose Nuclei	Adipose
13	chr8:69141200-69143400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr8:69141200-69143400	Enhancers	Brain Substantia Nigra	brain
15	chr8:69141200-69144000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr8:69141400-69143000	Enhancers	H9 Cell Line	embryonic stem cell
17	chr8:69141400-69143200	Enhancers	Brain Anterior Caudate	brain
18	chr8:69141400-69143800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr8:69141400-69143800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr8:69141800-69143000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr8:69142000-69143000	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr8:69142000-69145200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr8:69142000-69146000	Weak transcription	Brain Hippocampus Middle	brain
24	chr8:69142000-69151400	Weak transcription	Aorta	Aorta
25	chr8:69142400-69144200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr8:69142600-69143000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr8:69142600-69153400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr8:69142800-69143000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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