Variant report

Variant	rs159977
Chromosome Location	chr5:152728116-152728117
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1462115	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs149239	0.99[EUR][1000 genomes]
rs159760	0.99[EUR][1000 genomes]
rs159969	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159971	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs159974	0.99[EUR][1000 genomes]
rs159975	0.99[EUR][1000 genomes]
rs159976	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs188597	0.98[EUR][1000 genomes]
rs214122	0.99[EUR][1000 genomes]
rs217771	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2560240	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2560242	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs296171	1.00[CEU][hapmap];0.84[TSI][hapmap]
rs2973150	0.82[EUR][1000 genomes]
rs300329	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs300330	0.99[EUR][1000 genomes]
rs300333	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs300336	0.99[EUR][1000 genomes]
rs308269	0.89[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs308271	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs308272	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023676	chr5:151979253-152925064	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv537927	chr5:151979253-152925064	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1019051	chr5:152550863-153057896	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv868912	chr5:152582002-153095306	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1023125	chr5:152688178-152730408	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv883052	chr5:152696107-152749009	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv883053	chr5:152696107-152806220	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs159977	C5orf4	cis	parietal	SCAN
rs159977	NMUR2	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:152721200-152729000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:152726400-152729200	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr5:152727000-152729400	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr5:152727800-152728200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
5	chr5:152727800-152728600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
6	chr5:152728000-152729000	Weak transcription	H1 Cell Line	embryonic stem cell

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