Variant report

Variant	rs7035755
Chromosome Location	chr9:26945976-26945977
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr9:26945575-26948341	NB4	blood:	n/a	n/a
2	POLR2A	chr9:26945741-26948332	H1-hESC	embryonic stem cell:	n/a	n/a
3	GATA1	chr9:26945386-26948919	PBDE	blood:	n/a	chr9:26948836-26948857 chr9:26948839-26948850
4	POLR2A	chr9:26945574-26948342	GM12891	blood:	n/a	n/a
5	CHD1	chr9:26945731-26948413	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr9:26945760-26948285	Hela-S3	cervix:	n/a	n/a
7	BRCA1	chr9:26945941-26946028	H1-hESC	embryonic stem cell:	n/a	n/a
8	MYC	chr9:26945612-26948147	NB4	blood:	n/a	n/a
9	MXI1	chr9:26945295-26948354	SK-N-SH	brain:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:26891080..26894676-chr9:26945695..26949113,9	K562	blood:
2	chr9:26891080..26895841-chr9:26945501..26948974,8	K562	blood:
3	chr9:26890485..26893190-chr9:26945159..26948755,7	MCF-7	breast:
4	chr9:26882668..26884290-chr9:26943587..26946347,2	MCF-7	breast:
5	chr9:26943098..26949574-chr9:26949927..26957421,13	K562	blood:
6	chr9:26863474..26865685-chr9:26944202..26946970,2	K562	blood:
7	chr9:26890972..26893985-chr9:26945405..26948624,3	MCF-7	breast:
8	chr9:26945881..26949167-chr9:26974909..26976838,3	MCF-7	breast:
9	chr9:26920077..26923896-chr9:26945076..26948067,5	MCF-7	breast:

No data

Variant related genes	Relation type
IFT74	TF binding region
ENSG00000096872	Chromatin interaction
ENSG00000120159	Chromatin interaction
ENSG00000137055	Chromatin interaction
ENSG00000240306	Chromatin interaction
ENSG00000234676	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10511792	0.83[MKK][hapmap]
rs10511793	0.83[GIH][hapmap]
rs10812492	0.83[GIH][hapmap]
rs10967594	0.83[GIH][hapmap]
rs10967625	0.86[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12004732	1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12338262	0.85[CEU][hapmap];0.86[MEX][hapmap]
rs12352441	0.86[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16910873	0.83[MKK][hapmap]
rs16910888	0.90[GIH][hapmap]
rs17693955	0.92[CEU][hapmap]
rs59274950	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62542667	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62542672	0.82[AMR][1000 genomes]
rs62544443	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62544444	0.95[ASN][1000 genomes]
rs62544450	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62544451	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62544452	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6475948	0.88[MEX][hapmap]
rs7018962	0.83[MKK][hapmap]
rs7023230	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7039400	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7045881	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]
rs73436047	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7851339	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7851423	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7851582	0.88[EUR][1000 genomes]
rs7860542	0.85[CEU][hapmap]
rs7866718	0.83[ASN][1000 genomes]
rs7871097	0.90[GIH][hapmap]
rs7871286	0.86[GIH][hapmap]
rs7872881	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7035755	IFT74	cis	lymphoblastoid	seeQTL
rs7035755	C9orf82	cis	parietal	SCAN
rs7035755	C9orf82	cis	cerebellum	SCAN
rs7035755	IFT74	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26940000-26948400	Active TSS	GM12878-XiMat	blood
2	chr9:26943000-26946000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr9:26943000-26946200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr9:26944200-26946200	Enhancers	Primary T cells fromperipheralblood	blood
5	chr9:26944400-26946200	Flanking Active TSS	Dnd41	blood
6	chr9:26944600-26948400	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr9:26944800-26948000	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr9:26945000-26946200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr9:26945200-26946000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:26945200-26946000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr9:26945200-26946000	Enhancers	Fetal Heart	heart
12	chr9:26945200-26946000	Flanking Active TSS	NHDF-Ad	bronchial
13	chr9:26945200-26946000	Flanking Active TSS	NHEK	skin
14	chr9:26945200-26946200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:26945200-26946200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:26945200-26946200	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr9:26945200-26946200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr9:26945200-26946200	Flanking Active TSS	Hela-S3	cervix
19	chr9:26945200-26946400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr9:26945200-26946400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr9:26945200-26946400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:26945200-26946400	Flanking Active TSS	Liver	Liver
23	chr9:26945200-26946400	Flanking Active TSS	Brain Germinal Matrix	brain
24	chr9:26945200-26947800	Active TSS	HMEC	breast
25	chr9:26945200-26948000	Active TSS	NHLF	lung
26	chr9:26945200-26948200	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr9:26945200-26948200	Active TSS	K562	blood
28	chr9:26945200-26948400	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr9:26945200-26948400	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr9:26945400-26946000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr9:26945400-26946000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr9:26945400-26946000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:26945400-26946000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr9:26945400-26946000	Flanking Active TSS	A549	lung
35	chr9:26945400-26946000	Flanking Active TSS	HepG2	liver
36	chr9:26945400-26946200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr9:26945400-26946200	Flanking Active TSS	Colon Smooth Muscle	Colon
38	chr9:26945400-26946400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr9:26945400-26946400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr9:26945400-26946400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr9:26945400-26946400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr9:26945400-26946400	Enhancers	Small Intestine	intestine
43	chr9:26945400-26946400	Flanking Active TSS	HUVEC	blood vessel
44	chr9:26945400-26946400	Flanking Active TSS	NH-A	brain
45	chr9:26945400-26946400	Flanking Active TSS	Osteobl	bone
46	chr9:26945400-26946600	Flanking Active TSS	Brain Anterior Caudate	brain
47	chr9:26945400-26946800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr9:26945400-26946800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr9:26945400-26948000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr9:26945400-26948200	Active TSS	H1 Cell Line	embryonic stem cell

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