Variant report

Variant	rs7023154
Chromosome Location	chr9:15291834-15291835
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15283111..15284924-chr9:15291453..15293765,2	MCF-7	breast:
2	chr9:15290133..15292362-chr9:15306023..15308672,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155158	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1001829	0.87[CEU][hapmap]
rs10114494	0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10115392	0.86[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10118629	0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10121612	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10125948	0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10810370	0.82[CEU][hapmap];0.90[CHB][hapmap];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10810373	0.95[CEU][hapmap]
rs10961957	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10961960	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10961963	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10961965	0.90[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1122677	0.90[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17327373	0.90[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2382518	0.84[AMR][1000 genomes]
rs2382519	0.83[CEU][hapmap];0.91[CHB][hapmap];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2890998	0.82[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62570840	0.89[AMR][1000 genomes]
rs7022687	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7023864	0.83[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv2762797	chr9:15282415-15297028	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv969751	chr9:15287487-15294727	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7023154	C9orf52	cis	multi-tissue	Pritchard
rs7023154	C9orf52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15243000-15293400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr9:15254000-15293000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr9:15254200-15293000	Weak transcription	NHEK	skin
4	chr9:15254200-15295600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:15259200-15293400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr9:15273600-15293400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr9:15277000-15292200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr9:15277000-15293000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr9:15277600-15296800	Weak transcription	Gastric	stomach
10	chr9:15278000-15295200	Weak transcription	Pancreas	Pancrea
11	chr9:15279800-15293200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:15283600-15293800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr9:15285200-15293800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:15286800-15293200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr9:15286800-15293800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr9:15287000-15293600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr9:15287000-15294200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr9:15287400-15303600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr9:15287600-15292800	Weak transcription	Primary T cells from cord blood	blood
20	chr9:15287600-15293000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr9:15287600-15293000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr9:15287600-15293600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr9:15287600-15294000	Weak transcription	Small Intestine	intestine
24	chr9:15288600-15293400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr9:15288600-15293400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr9:15288600-15294200	Weak transcription	HepG2	liver
27	chr9:15288800-15293800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr9:15288800-15293800	Weak transcription	Fetal Lung	lung
29	chr9:15288800-15294800	Weak transcription	Lung	lung
30	chr9:15289000-15293200	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr9:15289000-15293400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:15289200-15292000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr9:15289200-15293200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr9:15289200-15293400	Weak transcription	Esophagus	oesophagus
35	chr9:15289200-15295400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr9:15289400-15292200	Enhancers	H1 Cell Line	embryonic stem cell
37	chr9:15289400-15292200	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr9:15289400-15292400	Enhancers	Fetal Intestine Small	intestine
39	chr9:15289400-15292400	Enhancers	Fetal Stomach	stomach
40	chr9:15289400-15293400	Weak transcription	NHLF	lung
41	chr9:15290000-15293400	Weak transcription	Ovary	ovary
42	chr9:15290000-15293400	Weak transcription	HSMM	muscle
43	chr9:15290200-15292400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr9:15290600-15293200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr9:15290600-15293400	Weak transcription	Fetal Kidney	kidney
46	chr9:15290800-15293800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr9:15290800-15294200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr9:15290800-15305600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr9:15290800-15306000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr9:15291000-15293800	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links