Variant report

Variant	rs2768285
Chromosome Location	chr9:108313636-108313637
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:108312149..108315123-chr9:108317166..108320384,3	K562	blood:
2	chr9:108311203..108313649-chr9:108317166..108319459,2	K562	blood:
3	chr9:108313005..108314954-chr9:108320273..108321938,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228317	Chromatin interaction
ENSG00000106692	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1018848	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1018849	0.93[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs1018850	1.00[YRI][hapmap]
rs1024366	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10820805	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10820806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10820807	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10820808	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10820816	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10991661	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10991662	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10991664	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10991666	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10991669	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10991675	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10991680	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10991686	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10991688	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11525961	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11535511	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12235779	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12554844	1.00[YRI][hapmap]
rs12555267	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]
rs1327351	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1329021	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1329022	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1576285	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16924672	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16924676	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1858744	1.00[ASW][hapmap];0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1928293	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1928294	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2010861	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2068266	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2518109	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2518110	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2518111	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2518113	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2518117	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2518118	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2518119	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2518121	1.00[YRI][hapmap]
rs2518122	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]
rs2518127	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2518132	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2518133	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2768278	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2768282	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2768284	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2768286	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2768287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2768288	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2768293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2768295	1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2768296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2904847	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4302902	0.97[ASN][1000 genomes]
rs56134629	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs72744254	0.85[ASN][1000 genomes]
rs72744266	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72744269	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs879115	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs879117	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs879118	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs885955	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
rs2768285	ZNF189	cis	parietal	SCAN
rs2768285	OR13D1	cis	cerebellum	SCAN
rs2768285	FKTN	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108279000-108317600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:108282400-108319800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr9:108282400-108319800	Weak transcription	Left Ventricle	heart
4	chr9:108282400-108319800	Weak transcription	Psoas Muscle	Psoas
5	chr9:108282600-108319800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:108292600-108319800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr9:108293800-108319800	Weak transcription	Liver	Liver
8	chr9:108294800-108319800	Weak transcription	Hela-S3	cervix
9	chr9:108295600-108319800	Weak transcription	Aorta	Aorta
10	chr9:108296400-108316200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr9:108297600-108319800	Weak transcription	NHLF	lung
12	chr9:108297800-108319200	Weak transcription	Dnd41	blood
13	chr9:108297800-108319800	Weak transcription	Adipose Nuclei	Adipose
14	chr9:108298000-108319800	Weak transcription	NHDF-Ad	bronchial
15	chr9:108298600-108316000	Weak transcription	Fetal Brain Female	brain
16	chr9:108298800-108314000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:108298800-108314400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:108298800-108319800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:108300200-108316200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr9:108301000-108319800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:108301400-108319800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr9:108302200-108319800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr9:108304400-108314200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr9:108304400-108319800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr9:108305000-108319800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr9:108305600-108314200	Weak transcription	Fetal Kidney	kidney
27	chr9:108305800-108319200	Weak transcription	GM12878-XiMat	blood
28	chr9:108305800-108319800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr9:108307200-108319800	Weak transcription	Ovary	ovary
30	chr9:108309000-108319800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr9:108309200-108319600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:108309200-108319800	Weak transcription	HMEC	breast
33	chr9:108309400-108319800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:108309600-108319800	Weak transcription	A549	lung
35	chr9:108310400-108319400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr9:108311000-108313800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:108312000-108319800	Weak transcription	HSMM	muscle
38	chr9:108312000-108319800	Weak transcription	NH-A	brain
39	chr9:108313400-108319800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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