Variant report

Variant	rs4413873
Chromosome Location	chr9:26987027-26987028
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10738762	0.95[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10757634	0.82[ASN][1000 genomes]
rs10757635	0.95[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10757636	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10812488	1.00[CEU][hapmap];0.81[CHB][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10812503	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10812504	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10812507	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10812508	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10812515	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10812516	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10812518	0.82[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10967645	1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs10967648	0.85[ASN][1000 genomes]
rs10967652	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.97[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10967670	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10967679	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs12337896	0.82[CHB][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1537639	0.86[ASN][1000 genomes]
rs1541144	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1819539	0.83[CHB][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1970187	0.88[ASN][1000 genomes]
rs2225720	0.83[CHB][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3758218	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4621911	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs59159685	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6475945	0.86[CEU][hapmap];0.82[JPT][hapmap]
rs6475947	0.86[CEU][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap]
rs6475954	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs7018585	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7020010	0.94[CHB][hapmap]
rs7032756	0.81[JPT][hapmap]
rs7034478	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7034670	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7035292	0.82[AMR][1000 genomes]
rs7038218	0.89[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7040505	0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7042133	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7042447	0.86[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7045339	0.81[ASN][1000 genomes]
rs7849248	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs7854191	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7856462	0.86[CEU][hapmap];0.82[JPT][hapmap]
rs7857669	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs7860542	0.82[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap]
rs7863476	0.90[CEU][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7868158	0.85[CEU][hapmap];0.87[JPT][hapmap]
rs7870787	0.89[CHB][hapmap]
rs7871668	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs7875068	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4413873	IFT74	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26957000-27024000	Weak transcription	Esophagus	oesophagus
2	chr9:26957200-27026600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr9:26957200-27040000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr9:26969000-26991200	Weak transcription	NHDF-Ad	bronchial
5	chr9:26970800-26990000	Weak transcription	Spleen	Spleen
6	chr9:26972200-26995000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr9:26972800-26990600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr9:26974200-27023600	Weak transcription	Fetal Brain Female	brain
9	chr9:26976200-27003600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr9:26976600-26996800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr9:26976800-26993000	Weak transcription	Osteobl	bone
12	chr9:26976800-27017800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr9:26977000-26997000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:26977200-27019400	Weak transcription	NH-A	brain
15	chr9:26977400-26992200	Weak transcription	HMEC	breast
16	chr9:26977400-26994400	Weak transcription	NHEK	skin
17	chr9:26977400-26998600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:26977800-26996800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr9:26977800-27026000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr9:26978000-26989400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr9:26979400-26993200	Weak transcription	Gastric	stomach
22	chr9:26979400-27024000	Weak transcription	Small Intestine	intestine
23	chr9:26979600-26992600	Weak transcription	Brain Germinal Matrix	brain
24	chr9:26980200-26987800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr9:26980400-26989400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr9:26981000-26992800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr9:26982800-26995200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr9:26982800-27023800	Weak transcription	Lung	lung
29	chr9:26983000-26987600	Strong transcription	Stomach Smooth Muscle	stomach
30	chr9:26983000-26987800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr9:26983000-26991200	Weak transcription	Fetal Intestine Small	intestine
32	chr9:26983200-26988000	Weak transcription	HUVEC	blood vessel
33	chr9:26983600-27023800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr9:26984200-26987200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:26984600-26987200	Strong transcription	Fetal Muscle Trunk	muscle
36	chr9:26984600-26987600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr9:26985000-26987200	Strong transcription	HSMMtube	muscle
38	chr9:26985000-26992400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr9:26985200-26987600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr9:26985200-26988800	Weak transcription	Placenta	Placenta
41	chr9:26985200-26992000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr9:26985200-26993000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr9:26985200-26993200	Weak transcription	Fetal Heart	heart
44	chr9:26985200-26993800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr9:26985200-26994200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr9:26985200-26994400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr9:26985200-26995400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr9:26985200-26996600	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr9:26985200-26997600	Weak transcription	Dnd41	blood
50	chr9:26985200-27011800	Weak transcription	Primary T helper cells fromperipheralblood	blood

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