Variant report

Variant	rs878567
Chromosome Location	chr5:63255991-63255992
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10042486	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10062933	0.95[EUR][1000 genomes]
rs1423691	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs358524	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs358526	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs358527	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs358528	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs378864	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs421321	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs428731	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6295	0.99[EUR][1000 genomes]
rs6449693	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6878612	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7448318	0.98[ASN][1000 genomes]
rs749099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7715837	0.96[CEU][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes]
rs970453	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598351	chr5:63124140-63751144	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs878567	RNF180	cis	cerebellum	SCAN
rs878567	DCAF4L1	trans	parietal	SCAN
rs878567	RGS7BP	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:63254000-63257000	Bivalent/Poised TSS	Fetal Brain Female	brain
2	chr5:63254600-63256000	Active TSS	H9 Cell Line	embryonic stem cell
3	chr5:63254600-63256400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:63254600-63257000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr5:63254600-63258400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
6	chr5:63254800-63256200	Active TSS	Brain Anterior Caudate	brain
7	chr5:63254800-63256400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:63254800-63258400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr5:63254800-63258800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
10	chr5:63254800-63259000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr5:63255400-63256000	Active TSS	Ovary	ovary
12	chr5:63255400-63256200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr5:63255400-63257600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:63255400-63258600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
15	chr5:63255600-63256000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
16	chr5:63255600-63256400	Bivalent Enhancer	Brain Germinal Matrix	brain
17	chr5:63255600-63256400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
18	chr5:63255600-63256600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr5:63255600-63256600	Bivalent Enhancer	Fetal Lung	lung
20	chr5:63255800-63256000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr5:63255800-63256000	Active TSS	Fetal Brain Male	brain
22	chr5:63255800-63256000	Weak transcription	Pancreas	Pancrea
23	chr5:63255800-63257200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr5:63255800-63258400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain

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