Variant report

Variant	rs3994562
Chromosome Location	chr9:100040031-100040032
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10115798	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10116404	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10217329	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10435866	0.84[EUR][1000 genomes]
rs10733584	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10733603	0.87[EUR][1000 genomes]
rs10739337	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10739365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759542	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10759547	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10759605	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759610	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759619	0.88[EUR][1000 genomes]
rs10759643	0.81[EUR][1000 genomes]
rs10817300	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10817306	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10817361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817403	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10817448	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10817492	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10817513	0.84[AMR][1000 genomes]
rs10817515	0.87[AMR][1000 genomes]
rs10981362	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10981528	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981537	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981551	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981557	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981560	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981625	0.91[EUR][1000 genomes]
rs10981848	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10981851	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10981889	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10981916	0.87[AMR][1000 genomes]
rs12378801	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12683119	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12683933	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1462086	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1462087	0.86[EUR][1000 genomes]
rs1462092	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1531439	0.94[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17331748	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1870859	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1935372	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2061634	0.86[EUR][1000 genomes]
rs2061635	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2255135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2401382	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2447287	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2447288	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2447289	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2447290	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2487874	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2487875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502646	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2615144	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2795363	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2795366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2795369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2795370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2818236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2818237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2818240	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2818241	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2818242	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2818244	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2888960	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3953688	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3994559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3994561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4345679	0.91[EUR][1000 genomes]
rs4433262	0.87[EUR][1000 genomes]
rs4437755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4524907	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4615708	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4645658	0.86[EUR][1000 genomes]
rs4742683	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742684	0.86[EUR][1000 genomes]
rs4743067	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4743074	0.91[EUR][1000 genomes]
rs4743075	0.89[EUR][1000 genomes]
rs4743080	0.82[EUR][1000 genomes]
rs56077563	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56306467	0.85[AMR][1000 genomes]
rs6478043	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6478044	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6478048	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6478051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020002	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7020144	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7023087	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7026287	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7026893	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7029749	0.84[EUR][1000 genomes]
rs7033212	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7033480	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7033642	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038353	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7047367	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs725228	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs725229	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs752243	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7847332	0.87[EUR][1000 genomes]
rs7850473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7855385	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7855956	0.88[EUR][1000 genomes]
rs7860264	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7867330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868052	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7868295	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7868312	0.82[EUR][1000 genomes]
rs7875158	0.83[EUR][1000 genomes]
rs7875296	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9299202	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9408859	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9409139	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3994562	RP11-520B13.4	cis	Esophagus Muscularis	GTEx
rs3994562	CCDC180	cis	Artery Tibial	GTEx
rs3994562	RP11-23J9.4	cis	Artery Tibial	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100002000-100040400	Weak transcription	Spleen	Spleen
2	chr9:100013000-100040400	Weak transcription	Brain Substantia Nigra	brain
3	chr9:100024400-100040600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:100024400-100042600	Weak transcription	Fetal Heart	heart
5	chr9:100025800-100050200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:100034800-100040400	Weak transcription	Fetal Brain Male	brain
7	chr9:100035000-100059600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr9:100036400-100042600	Weak transcription	Colonic Mucosa	Colon
9	chr9:100036800-100052200	Weak transcription	Stomach Mucosa	stomach
10	chr9:100037200-100050200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr9:100037400-100047000	Strong transcription	Fetal Muscle Trunk	muscle
12	chr9:100037800-100046600	Strong transcription	Stomach Smooth Muscle	stomach
13	chr9:100038000-100040200	Weak transcription	Thymus	Thymus
14	chr9:100038000-100040400	Weak transcription	Gastric	stomach
15	chr9:100038200-100040400	Weak transcription	Osteobl	bone
16	chr9:100038200-100040600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:100038200-100050600	Weak transcription	Esophagus	oesophagus
18	chr9:100038400-100041800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr9:100038600-100040200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr9:100038600-100040200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr9:100038600-100040400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr9:100038600-100040800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr9:100038600-100041400	Strong transcription	Brain Cingulate Gyrus	brain
24	chr9:100038600-100041400	Strong transcription	Fetal Intestine Small	intestine
25	chr9:100038600-100041600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr9:100038600-100042000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr9:100038600-100043800	Weak transcription	Psoas Muscle	Psoas
28	chr9:100038600-100044000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr9:100038600-100044400	Strong transcription	Fetal Intestine Large	intestine
30	chr9:100038600-100044600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr9:100038600-100045800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr9:100038600-100046800	Strong transcription	Brain Anterior Caudate	brain
33	chr9:100038600-100047600	Weak transcription	HepG2	liver
34	chr9:100038800-100040400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr9:100038800-100040800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr9:100038800-100041400	Strong transcription	Right Ventricle	heart
37	chr9:100038800-100041600	Strong transcription	Aorta	Aorta
38	chr9:100038800-100041600	Strong transcription	Brain Angular Gyrus	brain
39	chr9:100038800-100041600	Strong transcription	Fetal Stomach	stomach
40	chr9:100038800-100044800	Strong transcription	Primary B cells from peripheral blood	blood
41	chr9:100038800-100046400	Strong transcription	Ovary	ovary
42	chr9:100038800-100047200	Strong transcription	Liver	Liver
43	chr9:100038800-100050400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr9:100039000-100041400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr9:100039000-100043400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr9:100039000-100044000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr9:100039000-100046400	Strong transcription	Fetal Muscle Leg	muscle
48	chr9:100039000-100047000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr9:100039000-100047000	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr9:100039000-100050600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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