Variant report

Variant	rs12549883
Chromosome Location	chr8:69139792-69139793
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1058194	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10957423	0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs10957425	0.84[EUR][1000 genomes]
rs12541905	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12544661	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12546271	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12547567	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12547594	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12548558	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12549887	0.94[ASN][1000 genomes]
rs12549980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12549988	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12681348	0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs13257592	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13258486	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13262547	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.84[MKK][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13271545	0.83[EUR][1000 genomes]
rs13271692	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13272579	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13281136	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13282050	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1404600	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1404601	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1525054	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1525055	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1525056	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16934405	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1880538	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1917544	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2280636	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2280637	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2280638	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2280639	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2280640	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2280641	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35741702	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6472391	0.84[EUR][1000 genomes]
rs6472392	0.82[EUR][1000 genomes]
rs6984731	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7001824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7004629	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7005736	0.95[CHB][hapmap];0.84[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7819467	0.82[EUR][1000 genomes]
rs7821308	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7824298	0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs940664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][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
rs12549883	C9orf172	trans	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:69086000-69141600	Weak transcription	Fetal Muscle Leg	muscle
2	chr8:69103200-69141400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr8:69103200-69141800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr8:69105400-69141400	Weak transcription	Brain Hippocampus Middle	brain
5	chr8:69120600-69140000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr8:69125800-69141200	Weak transcription	Brain Substantia Nigra	brain
7	chr8:69128400-69141400	Weak transcription	Brain Anterior Caudate	brain
8	chr8:69129200-69141400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr8:69130000-69151800	Weak transcription	Lung	lung
10	chr8:69130200-69141400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr8:69130600-69141200	Weak transcription	Adipose Nuclei	Adipose
12	chr8:69130800-69143600	Weak transcription	HUVEC	blood vessel
13	chr8:69131000-69151200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr8:69131200-69140600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr8:69131200-69141600	Weak transcription	Fetal Brain Male	brain
16	chr8:69131200-69145000	Weak transcription	Fetal Stomach	stomach
17	chr8:69131400-69141800	Weak transcription	Brain Angular Gyrus	brain
18	chr8:69133000-69151800	Weak transcription	Left Ventricle	heart
19	chr8:69133400-69141200	Weak transcription	NHDF-Ad	bronchial
20	chr8:69134600-69141400	Weak transcription	Aorta	Aorta
21	chr8:69135200-69140200	Weak transcription	Spleen	Spleen
22	chr8:69135400-69141000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr8:69135400-69141800	Weak transcription	Right Atrium	heart
24	chr8:69136600-69141600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr8:69137000-69141400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr8:69137000-69141400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr8:69137400-69141400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr8:69138000-69140000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr8:69138200-69139800	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr8:69138200-69141400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr8:69138200-69141400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr8:69138200-69141800	Weak transcription	Psoas Muscle	Psoas
33	chr8:69138400-69141400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr8:69138800-69140600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr8:69138800-69141200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr8:69139200-69141200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr8:69139200-69141200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr8:69139200-69141200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr8:69139400-69141200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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