Variant report

Variant	rs6885327
Chromosome Location	chr5:120653398-120653399
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:120652965-120653401	A549	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000229855	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11960193	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12654352	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12658893	0.88[ASN][1000 genomes]
rs13162465	0.84[ASN][1000 genomes]
rs13186166	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2194082	0.84[ASN][1000 genomes]
rs2216616	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs34415831	0.87[ASN][1000 genomes]
rs34693873	0.84[ASN][1000 genomes]
rs3866711	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3909309	0.80[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3909355	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4409129	0.84[ASN][1000 genomes]
rs4895176	0.94[ASN][1000 genomes]
rs4895177	0.85[ASN][1000 genomes]
rs4997068	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs58413464	0.88[ASN][1000 genomes]
rs62379943	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62379950	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62379951	0.83[ASN][1000 genomes]
rs62379959	0.98[EUR][1000 genomes]
rs6879181	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6879185	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7717265	0.84[ASN][1000 genomes]
rs888874	0.84[ASN][1000 genomes]
rs966089	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599606	chr5:120219340-120776767	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv3402839	chr5:120286561-120667036	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv882797	chr5:120359319-120757262	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv33642	chr5:120380525-120848760	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv2754268	chr5:120398198-120745053	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1022981	chr5:120583543-120691755	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv2763911	chr5:120583555-120706241	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv518883	chr5:120591425-120708748	Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv599617	chr5:120608476-120670292	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv882800	chr5:120622200-120653398	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv882801	chr5:120622200-120656658	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv882802	chr5:120622200-120670292	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv965576	chr5:120648443-120661224	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
14	esv3469815	chr5:120648753-120654051	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6885327	CEP120	cis	cerebellum	SCAN
rs6885327	SRFBP1	cis	cerebellum	SCAN
rs6885327	SNCAIP	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:120651800-120654200	Weak transcription	Dnd41	blood
2	chr5:120653000-120653400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:120653200-120654400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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