Variant report

Variant	rs13301569
Chromosome Location	chr9:100655780-100655781
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100649531..100652518-chr9:100653450..100655843,2	MCF-7	breast:
2	chr9:100639021..100641102-chr9:100655728..100657284,2	MCF-7	breast:
3	chr9:100648546..100652838-chr9:100654754..100658082,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf156-2	chr9:100655088-100658103	XLOC_007800

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10113907	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10119795	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10818239	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11999801	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12003789	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12238579	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13300874	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1561958	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1561959	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4743140	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6478450	0.83[EUR][1000 genomes]
rs6586	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67449879	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7020644	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7033315	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7357707	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7853349	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7870125	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs874004	0.82[AMR][1000 genomes];0.80[EUR][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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13301569	C9orf156	cis	Skin Sun Exposed Lower leg	GTEx
rs13301569	C9orf156	cis	Thyroid	GTEx
rs13301569	C9orf156	cis	Esophagus Muscularis	GTEx
rs13301569	FOXE1	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100637600-100658000	Weak transcription	Gastric	stomach
2	chr9:100652400-100657400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr9:100652600-100659600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr9:100652600-100662400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr9:100652800-100657400	Weak transcription	Primary T cells from cord blood	blood
6	chr9:100652800-100660200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr9:100652800-100662000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr9:100652800-100662000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr9:100652800-100666600	Weak transcription	Fetal Lung	lung
10	chr9:100653000-100657800	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr9:100653000-100658200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr9:100653000-100660200	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr9:100653000-100660400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr9:100653000-100662600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr9:100653000-100663400	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr9:100653000-100667000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:100654200-100666600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr9:100654400-100657200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:100654600-100662400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:100655400-100655800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
21	chr9:100655600-100656000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:100655600-100656000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
23	chr9:100655600-100656000	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
24	chr9:100655600-100656000	ZNF genes & repeats	Adipose Nuclei	Adipose

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