Variant report

Variant	rs11999966
Chromosome Location	chr9:108376436-108376437
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10991660	0.81[CEU][hapmap];0.81[GIH][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap]
rs10991682	0.81[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs12002748	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12004019	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12004886	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12342071	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1808155	0.87[AFR][1000 genomes]
rs1854124	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2149592	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2149593	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2417627	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41277781	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66820447	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7033452	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs7034699	0.89[AFR][1000 genomes]
rs7034702	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7042000	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7858616	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7867012	1.00[ASW][hapmap];0.81[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs7872832	1.00[ASW][hapmap];0.81[CEU][hapmap];0.81[GIH][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs9657645	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[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	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

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108321600-108397200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr9:108333200-108400400	Weak transcription	HMEC	breast
3	chr9:108335400-108403400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr9:108338400-108403400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr9:108345600-108400000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr9:108347000-108399600	Weak transcription	Psoas Muscle	Psoas
7	chr9:108349400-108402200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr9:108350800-108403800	Weak transcription	Fetal Heart	heart
9	chr9:108352600-108382400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr9:108353600-108385600	Weak transcription	Fetal Kidney	kidney
11	chr9:108354400-108378200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:108354400-108385800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:108354400-108395800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr9:108354400-108395800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr9:108354400-108397200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:108354400-108397400	Weak transcription	Brain Hippocampus Middle	brain
17	chr9:108354400-108400000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr9:108354400-108403600	Weak transcription	Brain Substantia Nigra	brain
19	chr9:108354400-108412400	Weak transcription	Right Ventricle	heart
20	chr9:108354600-108377800	Weak transcription	Spleen	Spleen
21	chr9:108354600-108382400	Weak transcription	Fetal Brain Male	brain
22	chr9:108354600-108389600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr9:108354600-108395600	Weak transcription	Brain Angular Gyrus	brain
24	chr9:108354600-108397000	Weak transcription	Fetal Muscle Leg	muscle
25	chr9:108354600-108397200	Weak transcription	Aorta	Aorta
26	chr9:108354600-108401600	Weak transcription	GM12878-XiMat	blood
27	chr9:108354600-108412200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr9:108354800-108379400	Weak transcription	Fetal Intestine Small	intestine
29	chr9:108354800-108396400	Weak transcription	Fetal Stomach	stomach
30	chr9:108355200-108404200	Weak transcription	Brain Germinal Matrix	brain
31	chr9:108355200-108409200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr9:108355800-108396800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr9:108355800-108397200	Weak transcription	Ovary	ovary
34	chr9:108356000-108403800	Weak transcription	Fetal Thymus	thymus
35	chr9:108358200-108405000	Weak transcription	HUVEC	blood vessel
36	chr9:108359200-108384400	Weak transcription	NH-A	brain
37	chr9:108359800-108397000	Weak transcription	Liver	Liver
38	chr9:108360400-108385000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr9:108360600-108397000	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr9:108361000-108382200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr9:108361000-108397200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr9:108364000-108382200	Weak transcription	HSMM	muscle
43	chr9:108364800-108376600	Weak transcription	NHLF	lung
44	chr9:108366800-108382200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr9:108366800-108396800	Weak transcription	NHDF-Ad	bronchial
46	chr9:108366800-108397000	Weak transcription	Dnd41	blood
47	chr9:108366800-108397200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr9:108366800-108401400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr9:108366800-108403400	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr9:108366800-108405400	Weak transcription	Rectal Mucosa Donor 31	rectum

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