Variant report

Variant	rs7045881
Chromosome Location	chr9:26935996-26935997
allele	A/T
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
ENSG00000137055	Chromatin interaction
ENSG00000096872	Chromatin interaction
ENSG00000120159	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10511792	0.83[MKK][hapmap]
rs10511793	0.89[GIH][hapmap];0.89[MEX][hapmap]
rs10812492	0.89[GIH][hapmap]
rs10967594	0.89[GIH][hapmap];0.89[MEX][hapmap]
rs10967625	0.86[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12004732	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12338262	0.85[CEU][hapmap]
rs12352441	0.86[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16910873	0.83[MKK][hapmap]
rs16910888	0.96[GIH][hapmap];0.89[MEX][hapmap]
rs17693955	0.92[CEU][hapmap];0.82[GIH][hapmap];0.83[EUR][1000 genomes]
rs2184740	0.97[AFR][1000 genomes]
rs59274950	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62542667	0.83[EUR][1000 genomes]
rs62544361	0.83[EUR][1000 genomes]
rs62544362	0.83[EUR][1000 genomes]
rs62544443	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62544444	1.00[ASN][1000 genomes]
rs62544450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62544451	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62544452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6475948	0.83[GIH][hapmap]
rs7018962	0.83[MKK][hapmap]
rs7019692	0.84[ASN][1000 genomes]
rs7023230	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7035755	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7039400	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73436047	0.81[EUR][1000 genomes]
rs7851339	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851423	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7851582	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7860542	0.85[CEU][hapmap]
rs7866718	0.88[ASN][1000 genomes]
rs7871097	0.96[GIH][hapmap];0.89[MEX][hapmap]
rs7871286	0.93[GIH][hapmap];0.89[MEX][hapmap]
rs7872881	0.91[EUR][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	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

Variant related diseases (count:1)

Disease	PMID	Source
Schizophrenia	20185149	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7045881	IFT74	cis	lymphoblastoid	seeQTL
rs7045881	C9orf82	cis	cerebellum	SCAN
rs7045881	C9orf82	cis	parietal	SCAN
rs7045881	IFT74	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 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	chr9:26902800-26936600	Weak transcription	Spleen	Spleen
4	chr9:26905400-26938200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:26905800-26937400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr9:26906200-26936600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:26916800-26945200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr9:26917200-26936400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:26917200-26936600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:26920400-26937400	Weak transcription	Fetal Heart	heart
11	chr9:26925000-26936200	Weak transcription	Esophagus	oesophagus
12	chr9:26925000-26936400	Weak transcription	Gastric	stomach
13	chr9:26925000-26936600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:26925000-26936600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:26925000-26936600	Weak transcription	Lung	lung
16	chr9:26925800-26936400	Weak transcription	Brain Hippocampus Middle	brain
17	chr9:26925800-26945200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr9:26926000-26936000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr9:26926000-26936200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr9:26926000-26936200	Weak transcription	Ovary	ovary
21	chr9:26926000-26936200	Weak transcription	K562	blood
22	chr9:26926000-26936400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr9:26926000-26936400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr9:26926000-26936400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr9:26926000-26936400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr9:26926000-26936600	Weak transcription	Aorta	Aorta
27	chr9:26926000-26936600	Weak transcription	Left Ventricle	heart
28	chr9:26926000-26936600	Weak transcription	Right Ventricle	heart
29	chr9:26926000-26937600	Weak transcription	Brain Germinal Matrix	brain
30	chr9:26926000-26945200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr9:26926000-26945200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr9:26926000-26945400	Weak transcription	HSMMtube	muscle
33	chr9:26926200-26936200	Weak transcription	Colon Smooth Muscle	Colon
34	chr9:26926600-26936000	Weak transcription	Brain Angular Gyrus	brain
35	chr9:26926600-26937400	Weak transcription	Fetal Lung	lung
36	chr9:26926600-26937800	Weak transcription	Brain Anterior Caudate	brain
37	chr9:26926600-26941600	Weak transcription	HepG2	liver
38	chr9:26926600-26944200	Weak transcription	NHEK	skin
39	chr9:26926600-26945600	Weak transcription	Fetal Kidney	kidney
40	chr9:26927400-26937800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr9:26927400-26943800	Weak transcription	Pancreas	Pancrea
42	chr9:26927400-26945600	Weak transcription	Fetal Thymus	thymus
43	chr9:26927600-26936600	Weak transcription	Fetal Brain Female	brain
44	chr9:26927800-26937800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr9:26927800-26945600	Weak transcription	Colonic Mucosa	Colon
46	chr9:26928000-26937400	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr9:26928400-26937400	Weak transcription	Fetal Intestine Large	intestine
48	chr9:26928400-26938000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr9:26928400-26940200	Weak transcription	HUVEC	blood vessel
50	chr9:26928400-26941000	Weak transcription	Thymus	Thymus

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