Variant report

Variant	rs1024366
Chromosome Location	chr9:108399825-108399826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:108399430..108400714-chr9:108479607..108481929,7	MCF-7	breast:
2	chr9:108373781..108375674-chr9:108398914..108401614,2	MCF-7	breast:
3	chr9:108398780..108401386-chr9:108456796..108459594,2	K562	blood:
4	chr9:108395582..108398707-chr9:108398809..108401541,3	MCF-7	breast:
5	chr9:108398591..108401318-chr9:108456176..108458423,3	MCF-7	breast:
6	chr9:108396717..108400413-chr9:108407791..108411231,4	K562	blood:

Variant related genes	Relation type
ENSG00000095209	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1018848	0.83[AFR][1000 genomes]
rs1018849	1.00[CHB][hapmap]
rs1018850	1.00[YRI][hapmap]
rs10820806	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10820807	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10991661	0.92[CHB][hapmap];1.00[YRI][hapmap]
rs10991662	1.00[ASW][hapmap];0.84[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[YRI][hapmap]
rs10991664	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10991666	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10991669	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10991675	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10991680	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10991688	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11525961	0.88[EUR][1000 genomes]
rs12554844	1.00[YRI][hapmap]
rs12555267	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs1327351	1.00[ASW][hapmap];0.84[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.81[MEX][hapmap];1.00[YRI][hapmap]
rs1329022	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap]
rs16924672	0.85[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs16924676	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1858744	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs1928293	1.00[ASW][hapmap];0.84[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];1.00[YRI][hapmap]
rs1928294	0.93[CHB][hapmap];1.00[YRI][hapmap]
rs2010861	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2518109	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2518110	1.00[ASW][hapmap];0.84[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap]
rs2518117	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2518118	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2518119	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2518121	1.00[YRI][hapmap]
rs2518122	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]
rs2518127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2518132	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2518133	1.00[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2768278	0.85[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2768282	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2768284	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap]
rs2768285	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]
rs2768287	0.93[CHB][hapmap]
rs2768293	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2768295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2768296	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2904847	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs879115	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs879117	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs879118	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[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	nsv519023	chr9:108371549-108454745	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1024366	OR13D1	cis	cerebellum	SCAN
rs1024366	ZNF189	cis	parietal	SCAN
rs1024366	FKTN	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108333200-108400400	Weak transcription	HMEC	breast
2	chr9:108335400-108403400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr9:108338400-108403400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr9:108345600-108400000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr9:108349400-108402200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr9:108350800-108403800	Weak transcription	Fetal Heart	heart
7	chr9:108354400-108400000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr9:108354400-108403600	Weak transcription	Brain Substantia Nigra	brain
9	chr9:108354400-108412400	Weak transcription	Right Ventricle	heart
10	chr9:108354600-108401600	Weak transcription	GM12878-XiMat	blood
11	chr9:108354600-108412200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr9:108355200-108404200	Weak transcription	Brain Germinal Matrix	brain
13	chr9:108355200-108409200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr9:108356000-108403800	Weak transcription	Fetal Thymus	thymus
15	chr9:108358200-108405000	Weak transcription	HUVEC	blood vessel
16	chr9:108366800-108401400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:108366800-108403400	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr9:108366800-108405400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr9:108366800-108418200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr9:108366800-108418200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:108367200-108402800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr9:108367200-108403400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr9:108367400-108407800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr9:108372200-108402200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:108373200-108404600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr9:108383400-108403400	Weak transcription	Colon Smooth Muscle	Colon
27	chr9:108383600-108402000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:108384200-108403600	Weak transcription	Fetal Brain Female	brain
29	chr9:108384400-108401400	Weak transcription	Fetal Brain Male	brain
30	chr9:108384400-108403800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr9:108389600-108403200	Weak transcription	A549	lung
32	chr9:108391800-108404600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr9:108392000-108407000	Weak transcription	Fetal Lung	lung
34	chr9:108393600-108402400	Weak transcription	NHEK	skin
35	chr9:108393600-108402800	Weak transcription	Pancreas	Pancrea
36	chr9:108394600-108403600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr9:108396000-108401800	Weak transcription	Fetal Kidney	kidney
38	chr9:108396200-108403400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr9:108396200-108409200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr9:108396600-108403800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr9:108396800-108400200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr9:108396800-108400600	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr9:108397000-108400200	Strong transcription	Primary B cells from cord blood	blood
44	chr9:108397000-108400400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr9:108397000-108401400	Strong transcription	Fetal Muscle Leg	muscle
46	chr9:108397000-108401600	Strong transcription	Primary T cells from cord blood	blood
47	chr9:108397000-108401600	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr9:108397000-108401800	Strong transcription	Adipose Nuclei	Adipose
49	chr9:108397000-108402400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr9:108397200-108400000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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