Variant report

Variant	rs10738762
Chromosome Location	chr9:26934858-26934859
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:26934470..26938073-chr9:26945974..26949391,4	K562	blood:
2	chr9:26934470..26938073-chr9:26945974..26949091,3	K562	blood:
3	chr9:26891082..26893488-chr9:26933500..26937576,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000096872	Chromatin interaction
ENSG00000137055	Chromatin interaction
ENSG00000120159	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10511793	0.82[TSI][hapmap]
rs10757634	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10757635	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10757636	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10812482	0.83[AMR][1000 genomes]
rs10812487	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10812488	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10812492	0.85[TSI][hapmap]
rs10812494	0.80[JPT][hapmap]
rs10812503	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10812504	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10812507	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10812508	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10812515	0.85[AMR][1000 genomes]
rs10812518	0.83[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap]
rs10967548	0.83[EUR][1000 genomes]
rs10967549	0.83[EUR][1000 genomes]
rs10967551	0.82[EUR][1000 genomes]
rs10967556	0.85[EUR][1000 genomes]
rs10967586	0.89[JPT][hapmap]
rs10967594	0.82[TSI][hapmap]
rs10967629	0.86[ASN][1000 genomes]
rs10967632	0.86[ASN][1000 genomes]
rs10967635	0.88[CHD][hapmap]
rs10967645	0.94[CHB][hapmap]
rs10967649	0.91[CHD][hapmap]
rs10967652	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10967661	0.85[CHD][hapmap]
rs10967670	0.86[AMR][1000 genomes]
rs10967679	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs12004732	0.85[TSI][hapmap]
rs12236850	0.88[CHD][hapmap]
rs12337896	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes]
rs12342005	0.82[CEU][hapmap]
rs1541144	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1819539	0.89[CHB][hapmap];0.86[AMR][1000 genomes]
rs2184438	0.88[ASN][1000 genomes]
rs2184439	0.87[ASN][1000 genomes]
rs2225720	0.84[CEU][hapmap];0.89[CHB][hapmap];0.86[AMR][1000 genomes]
rs3737226	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs3739547	0.91[CHD][hapmap];0.80[JPT][hapmap]
rs3739550	0.80[JPT][hapmap]
rs3758218	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4413873	0.95[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4621911	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs59159685	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6475944	0.85[EUR][1000 genomes]
rs6475945	0.89[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6475946	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6475947	0.89[CEU][hapmap];0.83[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6475948	0.88[TSI][hapmap]
rs6475954	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs7018585	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7019034	0.80[JPT][hapmap]
rs7020010	1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs7032756	0.94[ASW][hapmap];0.84[CEU][hapmap];0.88[GIH][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap]
rs7033238	0.85[EUR][1000 genomes]
rs7034115	0.87[ASN][1000 genomes]
rs7034478	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7034670	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7035292	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7035447	0.88[CHD][hapmap]
rs7038218	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7040505	0.84[CEU][hapmap];0.83[CHB][hapmap];0.88[AMR][1000 genomes]
rs7042133	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7042447	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7849248	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs7854191	0.83[AMR][1000 genomes]
rs7856462	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7857466	0.80[JPT][hapmap]
rs7857481	0.83[EUR][1000 genomes]
rs7857669	0.88[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap]
rs7860542	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7863476	0.88[ASW][hapmap];0.84[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7868158	0.89[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7870787	0.94[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs7871097	0.82[TSI][hapmap]
rs7871286	0.82[TSI][hapmap]
rs7871668	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs7872496	0.89[JPT][hapmap]
rs7873073	0.90[CHD][hapmap];0.80[JPT][hapmap]
rs7875068	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9644870	0.91[CHD][hapmap]

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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10738762	IFT74	cis	lymphoblastoid	seeQTL
rs10738762	IFT74	cis	parietal	SCAN
rs10738762	IFT74	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26893400-26936400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:26893400-26936400	Weak transcription	Psoas Muscle	Psoas
3	chr9:26901200-26935800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:26902800-26936600	Weak transcription	Spleen	Spleen
5	chr9:26903000-26935200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr9:26903200-26935200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr9:26904600-26935200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:26905400-26938200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:26905800-26937400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr9:26906200-26936600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr9:26912800-26935000	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr9:26914600-26935600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr9:26916800-26945200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:26917200-26936400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:26917200-26936600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr9:26920400-26937400	Weak transcription	Fetal Heart	heart
17	chr9:26925000-26936200	Weak transcription	Esophagus	oesophagus
18	chr9:26925000-26936400	Weak transcription	Gastric	stomach
19	chr9:26925000-26936600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:26925000-26936600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:26925000-26936600	Weak transcription	Lung	lung
22	chr9:26925800-26936400	Weak transcription	Brain Hippocampus Middle	brain
23	chr9:26925800-26945200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr9:26926000-26936000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr9:26926000-26936200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr9:26926000-26936200	Weak transcription	Ovary	ovary
27	chr9:26926000-26936200	Weak transcription	K562	blood
28	chr9:26926000-26936400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr9:26926000-26936400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr9:26926000-26936400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr9:26926000-26936400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr9:26926000-26936600	Weak transcription	Aorta	Aorta
33	chr9:26926000-26936600	Weak transcription	Left Ventricle	heart
34	chr9:26926000-26936600	Weak transcription	Right Ventricle	heart
35	chr9:26926000-26937600	Weak transcription	Brain Germinal Matrix	brain
36	chr9:26926000-26945200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr9:26926000-26945200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr9:26926000-26945400	Weak transcription	HSMMtube	muscle
39	chr9:26926200-26936200	Weak transcription	Colon Smooth Muscle	Colon
40	chr9:26926600-26936000	Weak transcription	Brain Angular Gyrus	brain
41	chr9:26926600-26937400	Weak transcription	Fetal Lung	lung
42	chr9:26926600-26937800	Weak transcription	Brain Anterior Caudate	brain
43	chr9:26926600-26941600	Weak transcription	HepG2	liver
44	chr9:26926600-26944200	Weak transcription	NHEK	skin
45	chr9:26926600-26945600	Weak transcription	Fetal Kidney	kidney
46	chr9:26927400-26937800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr9:26927400-26943800	Weak transcription	Pancreas	Pancrea
48	chr9:26927400-26945600	Weak transcription	Fetal Thymus	thymus
49	chr9:26927600-26936600	Weak transcription	Fetal Brain Female	brain
50	chr9:26927800-26937800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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