Variant report

Variant	rs491322
Chromosome Location	chr9:15308154-15308155
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr9:15305818-15308209	IMR90	lung:	n/a	chr9:15306783-15306793
2	GATA3	chr9:15308141-15308229	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15306135..15309581-chr9:15420818..15425516,6	MCF-7	breast:

Variant related genes	Relation type
TTC39B	TF binding region
ENSG00000164975	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10115392	0.83[CHB][hapmap]
rs10118629	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs10121612	0.82[ASN][1000 genomes]
rs10125948	0.82[CHB][hapmap]
rs10810374	0.86[ASN][1000 genomes]
rs10961965	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs1215114	0.85[CEU][hapmap]
rs17327373	0.83[CHD][hapmap]
rs4008004	0.83[CHB][hapmap];0.87[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031340	chr9:15163004-15332769	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2761505	chr9:15274373-15319613	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv892624	chr9:15283761-15415461	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv613650	chr9:15296119-15378449	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv613651	chr9:15296355-15358157	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1015960	chr9:15296783-15380657	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv524849	chr9:15299590-15362057	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs491322	C9orf52	cis	multi-tissue	Pritchard
rs491322	TTC39B	cis	lymphoblastoid	seeQTL
rs491322	TTC39B	cis	Lymphoblastoid	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15307200-15309200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:15307800-15308400	Enhancers	Primary T killer memory cells from peripheral blood	blood
3	chr9:15307800-15308400	Enhancers	Fetal Intestine Large	intestine
4	chr9:15307800-15308600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:15307800-15308600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr9:15307800-15308600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr9:15307800-15308600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:15307800-15308600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr9:15307800-15308600	Enhancers	Duodenum Mucosa	Duodenum
10	chr9:15307800-15308600	Enhancers	Fetal Intestine Small	intestine
11	chr9:15307800-15308600	Enhancers	HSMM	muscle
12	chr9:15307800-15308800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr9:15307800-15308800	Enhancers	NHDF-Ad	bronchial
14	chr9:15307800-15309000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:15307800-15309000	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr9:15307800-15309000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:15307800-15309000	Enhancers	NH-A	brain
18	chr9:15307800-15309000	Enhancers	Osteobl	bone
19	chr9:15307800-15309200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr9:15307800-15309200	Enhancers	HMEC	breast
21	chr9:15307800-15309400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:15307800-15309600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr9:15307800-15310000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr9:15307800-15310400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr9:15307800-15310400	Enhancers	Muscle Satellite Cultured Cells	--
26	chr9:15307800-15310600	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr9:15307800-15310600	Enhancers	NHEK	skin
28	chr9:15307800-15311400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr9:15307800-15311600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr9:15308000-15308200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr9:15308000-15308400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr9:15308000-15308400	Weak transcription	HUVEC	blood vessel
33	chr9:15308000-15308600	Enhancers	HepG2	liver
34	chr9:15308000-15309000	Enhancers	Primary T cells from cord blood	blood
35	chr9:15308000-15309200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr9:15308000-15309600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr9:15308000-15309600	Weak transcription	Stomach Mucosa	stomach
38	chr9:15308000-15309800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr9:15308000-15310200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr9:15308000-15310400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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