Variant report

Variant	rs11167702
Chromosome Location	chr5:154200263-154200264
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:154200242..154202597-chr5:154233414..154235052,2	K562	blood:
2	chr5:154197564..154200404-chr5:154207941..154209684,2	MCF-7	breast:
3	chr5:154198864..154200743-chr5:154269155..154270734,2	K562	blood:
4	chr5:154133441..154135046-chr5:154198681..154200668,2	MCF-7	breast:
5	chr5:154193302..154196557-chr5:154196665..154201027,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263361	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10515726	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap]
rs11948782	0.87[ASN][1000 genomes]
rs17116316	1.00[CHB][hapmap]
rs17641488	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs286595	0.85[MEX][hapmap]
rs348735	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes]
rs348741	0.84[AMR][1000 genomes]
rs34951340	0.87[ASN][1000 genomes]
rs3867430	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55734017	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56226335	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs593637	1.00[CHB][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes]
rs6886571	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs903837	0.81[MEX][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	nsv830521	chr5:154147567-154244266	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11167702	C5orf4	cis	brain	BrainEAC
rs11167702	C5orf4	cis	intralobular white matter	BrainEAC
rs11167702	LARP1	cis	Whole Blood	GTEx
rs11167702	LARP1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154167000-154203000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:154169200-154204200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr5:154169200-154204200	Strong transcription	Dnd41	blood
4	chr5:154169400-154200800	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr5:154169400-154201400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:154169400-154204000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:154169400-154204200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:154169400-154204200	Strong transcription	Duodenum Mucosa	Duodenum
9	chr5:154169400-154205800	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr5:154169600-154202400	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr5:154169600-154204200	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr5:154170800-154201200	Strong transcription	Muscle Satellite Cultured Cells	--
13	chr5:154171000-154201000	Strong transcription	HSMM	muscle
14	chr5:154174000-154212200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:154174800-154204400	Strong transcription	Placenta	Placenta
16	chr5:154175200-154204400	Strong transcription	Osteobl	bone
17	chr5:154175200-154204600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:154177200-154202200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:154178200-154204000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:154181000-154201000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:154181000-154211600	Strong transcription	Brain Hippocampus Middle	brain
22	chr5:154181200-154204800	Strong transcription	Brain Cingulate Gyrus	brain
23	chr5:154182000-154211400	Strong transcription	Left Ventricle	heart
24	chr5:154187000-154211400	Strong transcription	Fetal Stomach	stomach
25	chr5:154187600-154204200	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr5:154187600-154204400	Strong transcription	Brain Germinal Matrix	brain
27	chr5:154188600-154202400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:154189400-154206000	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr5:154189800-154204600	Strong transcription	Lung	lung
30	chr5:154190000-154201200	Strong transcription	NHEK	skin
31	chr5:154190400-154204200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr5:154190600-154200800	Strong transcription	NHLF	lung
33	chr5:154190800-154201000	Strong transcription	Esophagus	oesophagus
34	chr5:154190800-154201200	Strong transcription	Gastric	stomach
35	chr5:154191000-154201200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:154191400-154201400	Strong transcription	Spleen	Spleen
37	chr5:154191600-154208600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:154191800-154200400	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr5:154191800-154200600	Weak transcription	Fetal Heart	heart
40	chr5:154191800-154206200	Strong transcription	Brain Anterior Caudate	brain
41	chr5:154191800-154211600	Strong transcription	Adipose Nuclei	Adipose
42	chr5:154192400-154204200	Strong transcription	Brain Substantia Nigra	brain
43	chr5:154192800-154200400	Strong transcription	Aorta	Aorta
44	chr5:154193000-154211800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:154193600-154201000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr5:154193800-154200400	Strong transcription	Primary B cells from cord blood	blood
47	chr5:154193800-154204200	Strong transcription	Fetal Thymus	thymus
48	chr5:154194000-154209400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr5:154195600-154201200	Strong transcription	Pancreas	Pancrea
50	chr5:154195600-154204600	Strong transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links