Variant report

Variant	rs925485
Chromosome Location	chr9:100619561-100619562
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100614821..100616567-chr9:100616970..100619601,2	MCF-7	breast:
2	chr9:100619175..100621925-chr9:100624139..100627052,3	K562	blood:
3	chr9:100602066..100604948-chr9:100618492..100620676,2	K562	blood:
4	chr9:100619175..100621925-chr9:100624139..100625780,2	K562	blood:

Variant related genes	Relation type
ENSG00000178919	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10739513	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759960	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10760017	1.00[ASN][1000 genomes]
rs10983975	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1348386	0.95[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1465965	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867279	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1912998	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3021523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743138	0.95[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6478423	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024345	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7046645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048394	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7848950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7849497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859751	0.91[CEU][hapmap];0.81[AMR][1000 genomes]
rs7870540	0.81[AMR][1000 genomes]
rs7870795	0.91[CEU][hapmap];0.81[AMR][1000 genomes]
rs7870871	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs894672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907576	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs907578	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907579	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907580	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907582	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973473	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv6627	chr9:100576258-100621034	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs925485	C9orf156	cis	Temporal Cortex	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100617600-100620000	Weak transcription	Pancreas	Pancrea
2	chr9:100619200-100619600	Enhancers	A549	lung
3	chr9:100619200-100619800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
4	chr9:100619200-100619800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
5	chr9:100619200-100619800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr9:100619200-100620000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:100619200-100620200	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:100619200-100620800	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:100619200-100620800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
10	chr9:100619200-100620800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
11	chr9:100619400-100619600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
12	chr9:100619400-100620000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:100619400-100620800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr9:100619400-100620800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived

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