Variant report

Variant	rs10978172
Chromosome Location	chr9:108383428-108383429
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:108382770..108384900-chr9:108386562..108388867,2	K562	blood:
2	chr9:108379028..108381759-chr9:108381935..108385962,3	K562	blood:
3	chr9:108383132..108387217-chr9:108389992..108393147,4	K562	blood:
4	chr9:108377937..108380528-chr9:108381608..108383435,2	K562	blood:

Variant related genes	Relation type
ENSG00000106692	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1048215	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10491809	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10816281	1.00[CEU][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10816283	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10816285	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10816286	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10816287	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10816288	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10816289	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]
rs10820804	1.00[CEU][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10820811	0.91[CEU][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10820814	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10820815	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10978169	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10978176	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]
rs10978177	0.89[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10978179	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10991659	1.00[CEU][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10991673	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10991677	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10991679	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11562356	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12336250	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12336844	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12337780	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12345599	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12352975	1.00[CEU][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1327352	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1327355	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1887367	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2296750	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2417625	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28542455	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28851907	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3750500	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3793639	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3818598	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs55798036	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7023302	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7023520	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7033138	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7033165	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7034149	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7037104	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7037141	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7037218	0.91[CEU][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7038407	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7045862	0.83[YRI][hapmap]
rs7047791	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72744263	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72744264	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7852541	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7854411	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7856617	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7857186	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs997319	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[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:82 , 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	chr9:108353600-108385600	Weak transcription	Fetal Kidney	kidney
10	chr9:108354400-108385800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr9:108354400-108395800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr9:108354400-108395800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr9:108354400-108397200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:108354400-108397400	Weak transcription	Brain Hippocampus Middle	brain
15	chr9:108354400-108400000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr9:108354400-108403600	Weak transcription	Brain Substantia Nigra	brain
17	chr9:108354400-108412400	Weak transcription	Right Ventricle	heart
18	chr9:108354600-108389600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr9:108354600-108395600	Weak transcription	Brain Angular Gyrus	brain
20	chr9:108354600-108397000	Weak transcription	Fetal Muscle Leg	muscle
21	chr9:108354600-108397200	Weak transcription	Aorta	Aorta
22	chr9:108354600-108401600	Weak transcription	GM12878-XiMat	blood
23	chr9:108354600-108412200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr9:108354800-108396400	Weak transcription	Fetal Stomach	stomach
25	chr9:108355200-108404200	Weak transcription	Brain Germinal Matrix	brain
26	chr9:108355200-108409200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr9:108355800-108396800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr9:108355800-108397200	Weak transcription	Ovary	ovary
29	chr9:108356000-108403800	Weak transcription	Fetal Thymus	thymus
30	chr9:108358200-108405000	Weak transcription	HUVEC	blood vessel
31	chr9:108359200-108384400	Weak transcription	NH-A	brain
32	chr9:108359800-108397000	Weak transcription	Liver	Liver
33	chr9:108360400-108385000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr9:108360600-108397000	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr9:108361000-108397200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr9:108366800-108396800	Weak transcription	NHDF-Ad	bronchial
37	chr9:108366800-108397000	Weak transcription	Dnd41	blood
38	chr9:108366800-108397200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr9:108366800-108401400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr9:108366800-108403400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr9:108366800-108405400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr9:108366800-108418200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr9:108366800-108418200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr9:108367200-108384600	Weak transcription	Fetal Lung	lung
45	chr9:108367200-108396200	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr9:108367200-108396800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr9:108367200-108399600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr9:108367200-108399600	Weak transcription	Fetal Intestine Large	intestine
49	chr9:108367200-108402800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr9:108367200-108403400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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