Variant report

Variant	rs2518122
Chromosome Location	chr9:108336070-108336071
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	chr9:108330989..108333120-chr9:108334347..108336541,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1018848	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1018849	1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1018850	1.00[YRI][hapmap]
rs1024366	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10820805	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10820806	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10820807	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10820808	0.87[ASN][1000 genomes]
rs10820816	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10991661	0.92[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10991662	1.00[ASW][hapmap];0.84[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10991664	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10991666	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10991669	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10991675	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10991680	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10991686	0.86[ASN][1000 genomes]
rs10991688	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11525961	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11535511	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12235779	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12554844	1.00[YRI][hapmap]
rs12555267	0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs1327351	1.00[ASW][hapmap];0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1329021	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1329022	0.84[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs1576285	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16924672	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16924676	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1858744	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1928293	1.00[ASW][hapmap];0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1928294	0.93[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2010861	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2068266	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2518109	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2518110	1.00[ASW][hapmap];0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2518111	0.95[ASN][1000 genomes]
rs2518113	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2518117	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2518118	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2518119	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2518121	1.00[YRI][hapmap]
rs2518127	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2518132	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2518133	1.00[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2768278	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2768282	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2768284	0.84[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2768285	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2768286	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2768287	0.93[CHB][hapmap];0.81[JPT][hapmap];0.96[ASN][1000 genomes]
rs2768288	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2768293	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2768295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2768296	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2904847	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4302902	0.95[ASN][1000 genomes]
rs56134629	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72744254	0.83[ASN][1000 genomes]
rs72744266	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72744269	0.96[ASN][1000 genomes]
rs879115	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs879117	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs879118	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs885955	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][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	nsv1049133	chr9:108292302-108356068	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2518122	ZNF189	cis	parietal	SCAN
rs2518122	FKTN	cis	parietal	SCAN
rs2518122	OR13D1	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108321600-108336800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr9:108321600-108336800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr9:108321600-108338000	Weak transcription	Colon Smooth Muscle	Colon
4	chr9:108321600-108353600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:108321600-108354000	Weak transcription	Right Ventricle	heart
6	chr9:108321600-108360200	Weak transcription	HSMM	muscle
7	chr9:108321600-108397200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr9:108324800-108353800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr9:108325400-108337800	Weak transcription	Dnd41	blood
10	chr9:108325400-108339200	Weak transcription	Fetal Brain Male	brain
11	chr9:108325400-108357200	Weak transcription	A549	lung
12	chr9:108325600-108336600	Weak transcription	Fetal Lung	lung
13	chr9:108325600-108353200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr9:108325600-108353200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr9:108325600-108353800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:108325800-108353800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr9:108326000-108338200	Weak transcription	Ovary	ovary
18	chr9:108328000-108372800	Weak transcription	NHEK	skin
19	chr9:108330800-108366200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr9:108331000-108337400	Weak transcription	Adipose Nuclei	Adipose
21	chr9:108331200-108340000	Weak transcription	NH-A	brain
22	chr9:108332800-108337200	Weak transcription	Osteobl	bone
23	chr9:108333200-108337800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr9:108333200-108338200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr9:108333200-108400400	Weak transcription	HMEC	breast
26	chr9:108333400-108336800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr9:108333400-108352600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr9:108333400-108352600	Weak transcription	Fetal Kidney	kidney
29	chr9:108333600-108337600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:108334000-108337200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr9:108334200-108368200	Weak transcription	Gastric	stomach
32	chr9:108334400-108336800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr9:108334600-108337800	Weak transcription	Fetal Intestine Large	intestine
34	chr9:108334600-108338400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:108334800-108337400	Weak transcription	Brain Anterior Caudate	brain
36	chr9:108334800-108353000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr9:108335000-108336600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr9:108335000-108336800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:108335000-108336800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr9:108335000-108337200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr9:108335000-108337400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr9:108335000-108338400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr9:108335000-108339800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr9:108335000-108352200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr9:108335000-108352600	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr9:108335000-108352600	Weak transcription	Brain Hippocampus Middle	brain
47	chr9:108335000-108353000	Weak transcription	Aorta	Aorta
48	chr9:108335200-108336600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr9:108335200-108337000	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr9:108335200-108337200	Weak transcription	Liver	Liver

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