Variant report

Variant	rs3429
Chromosome Location	chr9:27062721-27062722
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10283643	1.00[CHB][hapmap]
rs10511793	1.00[CHB][hapmap]
rs10511795	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs10511797	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs10812492	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10812500	1.00[CHB][hapmap]
rs10967593	1.00[CHB][hapmap]
rs10967594	1.00[CHB][hapmap]
rs10967624	1.00[CHB][hapmap]
rs10967625	1.00[CHB][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs10967634	1.00[CHB][hapmap]
rs10967639	1.00[CHB][hapmap]
rs10967640	1.00[CHB][hapmap]
rs1161603	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11788136	1.00[CHB][hapmap]
rs12001845	1.00[CHB][hapmap]
rs12005388	1.00[CHB][hapmap]
rs12337860	1.00[CHB][hapmap]
rs12338678	1.00[CHB][hapmap]
rs12339162	1.00[CHB][hapmap]
rs12340500	1.00[CHB][hapmap]
rs12342005	1.00[CHB][hapmap]
rs12343345	1.00[CHB][hapmap]
rs12345094	1.00[CHB][hapmap]
rs12349359	1.00[CHB][hapmap]
rs12352441	1.00[CHB][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs12352603	1.00[CHB][hapmap]
rs12352631	1.00[CHB][hapmap]
rs12554485	1.00[CHB][hapmap]
rs13293051	1.00[CHB][hapmap]
rs1541145	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs1591356	0.90[ASN][1000 genomes]
rs16910888	1.00[CHB][hapmap]
rs16910895	1.00[CHB][hapmap]
rs16911083	1.00[CHB][hapmap]
rs17694140	1.00[CHB][hapmap]
rs17694300	1.00[CHB][hapmap]
rs17694306	1.00[CHB][hapmap]
rs17694549	1.00[CHB][hapmap]
rs17694631	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17694796	1.00[CHB][hapmap]
rs17755887	1.00[CHB][hapmap]
rs17755911	1.00[CHB][hapmap]
rs17756179	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs17756299	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs17756599	1.00[CHB][hapmap]
rs17756667	1.00[CHB][hapmap]
rs17756685	1.00[CHB][hapmap]
rs2027124	1.00[CHB][hapmap]
rs2152063	1.00[CHB][hapmap]
rs2991949	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs57770546	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs596427	1.00[CHB][hapmap]
rs60130669	0.80[AFR][1000 genomes]
rs615532	1.00[CHB][hapmap]
rs62542663	0.90[AFR][1000 genomes]
rs62542665	0.90[AFR][1000 genomes]
rs62542667	0.95[AFR][1000 genomes]
rs62542669	0.95[AFR][1000 genomes]
rs62542670	0.95[AFR][1000 genomes]
rs62542672	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62542704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62542705	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62542706	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62542707	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62542708	0.95[AFR][1000 genomes]
rs62546685	0.90[AFR][1000 genomes]
rs625630	0.81[ASN][1000 genomes]
rs627339	0.81[ASN][1000 genomes]
rs639826	0.81[ASN][1000 genomes]
rs6475948	1.00[CHB][hapmap]
rs6475959	1.00[CHB][hapmap]
rs6475963	1.00[CHB][hapmap]
rs6475966	1.00[CHB][hapmap]
rs6475968	1.00[CHB][hapmap]
rs7030424	1.00[YRI][hapmap]
rs7037860	1.00[CHB][hapmap]
rs7038875	0.80[AFR][1000 genomes]
rs7039400	1.00[CHB][hapmap]
rs7040516	1.00[CHB][hapmap]
rs7040772	1.00[CHB][hapmap]
rs7042003	1.00[CHB][hapmap]
rs7042119	1.00[CHB][hapmap]
rs7044842	1.00[CHB][hapmap]
rs73436012	0.90[AFR][1000 genomes]
rs73436044	0.90[AFR][1000 genomes]
rs73436047	0.95[AFR][1000 genomes]
rs73438223	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73438278	0.80[AFR][1000 genomes]
rs73438282	0.80[AFR][1000 genomes]
rs73438302	0.80[AFR][1000 genomes]
rs73440204	0.80[AFR][1000 genomes]
rs73440205	0.80[AFR][1000 genomes]
rs73440214	0.80[AFR][1000 genomes]
rs73440217	0.80[AFR][1000 genomes]
rs7847280	1.00[CHB][hapmap]
rs7854048	1.00[CHB][hapmap]
rs7865596	0.90[AFR][1000 genomes]
rs7865919	0.80[AFR][1000 genomes]
rs7871097	1.00[CHB][hapmap]
rs7871178	1.00[CHB][hapmap]
rs7871286	1.00[CHB][hapmap]
rs7873019	1.00[CHB][hapmap]
rs7873161	1.00[CHB][hapmap]
rs7873329	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528614	chr9:26893662-27074233	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv517269	chr9:26945976-27137242	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv892862	chr9:26956663-27190655	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv466334	chr9:27028947-27098940	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv613944	chr9:27028947-27098940	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3429	IFT74	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26985200-27063800	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr9:27009800-27070000	Weak transcription	Psoas Muscle	Psoas
3	chr9:27014400-27068200	Weak transcription	Fetal Heart	heart
4	chr9:27018400-27065200	Weak transcription	Osteobl	bone
5	chr9:27024400-27082600	Weak transcription	Gastric	stomach
6	chr9:27024600-27064400	Weak transcription	Colonic Mucosa	Colon
7	chr9:27024600-27075800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr9:27024600-27078600	Weak transcription	Aorta	Aorta
9	chr9:27024600-27079000	Weak transcription	Pancreas	Pancrea
10	chr9:27024600-27082400	Weak transcription	Primary T cells from cord blood	blood
11	chr9:27024600-27083400	Weak transcription	Left Ventricle	heart
12	chr9:27024600-27085000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr9:27024600-27086800	Weak transcription	Right Ventricle	heart
14	chr9:27024800-27094800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:27025200-27064800	Weak transcription	Fetal Brain Female	brain
16	chr9:27025200-27078000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr9:27025400-27063600	Weak transcription	Brain Substantia Nigra	brain
18	chr9:27025400-27066800	Weak transcription	Brain Anterior Caudate	brain
19	chr9:27025400-27075600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr9:27037000-27069600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:27038000-27085000	Weak transcription	Brain Hippocampus Middle	brain
22	chr9:27038200-27065400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr9:27042400-27063600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr9:27046600-27068000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr9:27048800-27076200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr9:27049000-27065800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr9:27049400-27067200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr9:27049400-27072600	Weak transcription	Fetal Muscle Leg	muscle
29	chr9:27049600-27063400	Weak transcription	Thymus	Thymus
30	chr9:27049600-27063600	Weak transcription	Primary B cells from cord blood	blood
31	chr9:27049600-27066800	Weak transcription	Colon Smooth Muscle	Colon
32	chr9:27049800-27071600	Weak transcription	Fetal Stomach	stomach
33	chr9:27053800-27063400	Weak transcription	Fetal Lung	lung
34	chr9:27053800-27086800	Weak transcription	HSMM	muscle
35	chr9:27054000-27065000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr9:27054600-27063400	Weak transcription	HSMMtube	muscle
37	chr9:27055000-27067200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr9:27055200-27063400	Weak transcription	NHEK	skin
39	chr9:27055200-27064000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr9:27055200-27087000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr9:27057400-27063800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr9:27057400-27083000	Weak transcription	Liver	Liver
43	chr9:27057600-27064400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr9:27058000-27063800	Weak transcription	Duodenum Mucosa	Duodenum
45	chr9:27058200-27062800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr9:27058200-27065600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr9:27058400-27069600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr9:27058400-27075200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr9:27059400-27068000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr9:27060200-27063000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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