Variant report

Variant	rs12555267
Chromosome Location	chr9:108233175-108233176
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108231365..108233350-chr9:108238200..108241165,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1018848	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1018849	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1024366	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs10820805	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10820806	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10820807	0.85[JPT][hapmap];0.82[AMR][1000 genomes]
rs10820808	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10820816	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10991661	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10991662	0.84[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10991664	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10991666	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10991669	0.85[JPT][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs10991675	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.91[TSI][hapmap];0.98[ASN][1000 genomes]
rs10991680	0.91[ASN][1000 genomes]
rs10991686	0.82[ASN][1000 genomes]
rs10991688	0.92[ASN][1000 genomes]
rs11535511	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12235779	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1327351	0.84[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1329021	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1329022	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1576285	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16924672	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs16924676	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1858744	0.84[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1928293	0.84[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1928294	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2068266	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2518110	0.84[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2518111	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2518113	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2518117	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2518118	0.92[ASN][1000 genomes]
rs2518119	0.94[ASN][1000 genomes]
rs2518122	0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs2518127	0.86[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs2518132	0.86[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap]
rs2518133	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs2768278	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2768282	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs2768284	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2768285	0.93[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.96[ASN][1000 genomes]
rs2768286	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2768287	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2768288	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2768293	0.98[ASN][1000 genomes]
rs2768295	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2768296	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2904847	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.97[ASN][1000 genomes]
rs4302902	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56134629	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72744254	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72744266	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72744269	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs885955	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1053973	chr9:108199177-108300186	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv615115	chr9:108205262-108298183	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv893692	chr9:108218852-108320988	ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
5	nsv1050141	chr9:108219667-108317424	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12555267	OR13D1	cis	cerebellum	SCAN
rs12555267	FKTN	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108211000-108248000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:108212200-108234800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr9:108214600-108309800	Weak transcription	HUVEC	blood vessel
4	chr9:108220200-108243400	Weak transcription	Colon Smooth Muscle	Colon
5	chr9:108220400-108237400	Weak transcription	Brain Hippocampus Middle	brain
6	chr9:108220400-108252600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr9:108220600-108237000	Weak transcription	Pancreas	Pancrea
8	chr9:108220600-108237400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr9:108220800-108237000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:108220800-108237600	Weak transcription	Aorta	Aorta
11	chr9:108221000-108233200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr9:108221000-108235400	Weak transcription	Gastric	stomach
13	chr9:108221000-108236200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:108221000-108237400	Weak transcription	Brain Substantia Nigra	brain
15	chr9:108221000-108257000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:108221000-108257200	Weak transcription	Fetal Stomach	stomach
17	chr9:108221000-108266000	Weak transcription	NHEK	skin
18	chr9:108221000-108277200	Weak transcription	Left Ventricle	heart
19	chr9:108221200-108235000	Weak transcription	Spleen	Spleen
20	chr9:108221800-108236600	Weak transcription	Small Intestine	intestine
21	chr9:108221800-108238200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr9:108222000-108237600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr9:108222200-108237400	Weak transcription	Psoas Muscle	Psoas
24	chr9:108222200-108259000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr9:108222200-108277000	Weak transcription	Ovary	ovary
26	chr9:108222400-108236800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr9:108222400-108242200	Weak transcription	Brain Anterior Caudate	brain
28	chr9:108222400-108259000	Weak transcription	HSMMtube	muscle
29	chr9:108222600-108311400	Weak transcription	Fetal Heart	heart
30	chr9:108223200-108252600	Weak transcription	K562	blood
31	chr9:108223600-108255200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr9:108224800-108244000	Weak transcription	Fetal Brain Male	brain
33	chr9:108225000-108237000	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr9:108225000-108249200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr9:108225800-108233600	Strong transcription	A549	lung
36	chr9:108226400-108234800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr9:108226600-108233600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr9:108226600-108234000	Strong transcription	NHDF-Ad	bronchial
39	chr9:108226600-108235600	Strong transcription	HepG2	liver
40	chr9:108226800-108235400	Strong transcription	HSMM	muscle
41	chr9:108227000-108233600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr9:108227400-108271600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:108227600-108278400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr9:108227800-108239200	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr9:108228000-108258800	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr9:108228200-108235800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:108228200-108237400	Weak transcription	Liver	Liver
48	chr9:108228200-108237600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr9:108228200-108250200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr9:108228400-108238600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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