Variant report

Variant	rs10816289
Chromosome Location	chr9:108397016-108397017
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:108395259..108397968-chr9:108400674..108403020,2	MCF-7	breast:
2	chr9:108396793..108398414-chr9:108407668..108410214,2	K562	blood:
3	chr9:108396366..108398534-chr9:108458632..108460449,2	K562	blood:
4	chr9:108396717..108400413-chr9:108407791..108411231,4	K562	blood:
5	chr9:108395582..108398707-chr9:108398809..108401541,3	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1048215	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10491809	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10816281	1.00[CEU][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10816283	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10816285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10816286	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10816287	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10816288	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820804	1.00[CEU][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10820811	0.91[CEU][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10820814	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10820815	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10978169	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10978172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10978176	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978177	0.89[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10978179	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10991659	1.00[CEU][hapmap];0.81[JPT][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10991673	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10991677	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10991679	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11562356	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12336250	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12336844	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12337780	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12345599	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12352975	1.00[CEU][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1327352	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1327355	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1887367	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2296750	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2417625	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28542455	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28851907	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3750500	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3793639	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3818598	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[YRI][hapmap];0.81[EUR][1000 genomes]
rs55798036	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6477448	0.82[YRI][hapmap]
rs7023302	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7023520	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7033138	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7033165	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7034149	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7037104	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7037141	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7037218	0.91[CEU][hapmap];0.86[JPT][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7038407	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7045862	0.91[YRI][hapmap]
rs7047791	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72744263	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72744264	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7852541	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7854411	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7856617	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7857186	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs997319	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[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

No data

Chromatin state (count:86 , 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	chr9:108354400-108397200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:108354400-108397400	Weak transcription	Brain Hippocampus Middle	brain
11	chr9:108354400-108400000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr9:108354400-108403600	Weak transcription	Brain Substantia Nigra	brain
13	chr9:108354400-108412400	Weak transcription	Right Ventricle	heart
14	chr9:108354600-108397200	Weak transcription	Aorta	Aorta
15	chr9:108354600-108401600	Weak transcription	GM12878-XiMat	blood
16	chr9:108354600-108412200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr9:108355200-108404200	Weak transcription	Brain Germinal Matrix	brain
18	chr9:108355200-108409200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr9:108355800-108397200	Weak transcription	Ovary	ovary
20	chr9:108356000-108403800	Weak transcription	Fetal Thymus	thymus
21	chr9:108358200-108405000	Weak transcription	HUVEC	blood vessel
22	chr9:108361000-108397200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr9:108366800-108397200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr9:108366800-108401400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr9:108366800-108403400	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr9:108366800-108405400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr9:108366800-108418200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr9:108366800-108418200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:108367200-108399600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr9:108367200-108399600	Weak transcription	Fetal Intestine Large	intestine
31	chr9:108367200-108402800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr9:108367200-108403400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr9:108367400-108407800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:108372200-108402200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:108373200-108398800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr9:108373200-108404600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr9:108373400-108398600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr9:108373600-108397400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:108374200-108397400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr9:108383400-108403400	Weak transcription	Colon Smooth Muscle	Colon
41	chr9:108383600-108402000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr9:108384200-108403600	Weak transcription	Fetal Brain Female	brain
43	chr9:108384400-108401400	Weak transcription	Fetal Brain Male	brain
44	chr9:108384400-108403800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr9:108386000-108397600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr9:108387400-108399400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr9:108389600-108403200	Weak transcription	A549	lung
48	chr9:108391800-108404600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr9:108392000-108407000	Weak transcription	Fetal Lung	lung
50	chr9:108393400-108398800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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