Variant report

Variant	rs11070359
Chromosome Location	chr15:42358580-42358581
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:42358395..42359373-chr15:42376220..42377263,7	MCF-7	breast:
2	chr15:42353361..42355428-chr15:42357307..42359309,2	K562	blood:
3	chr15:42358521..42359496-chr15:42376228..42377794,11	MCF-7	breast:
4	chr15:42358307..42359354-chr15:42376475..42377334,4	K562	blood:
5	chr15:42358458..42359350-chr15:42425452..42426798,6	MCF-7	breast:
6	chr15:42358521..42359538-chr15:42376137..42377161,21	MCF-7	breast:
7	chr15:42357824..42359039-chr15:42425603..42426626,4	MCF-7	breast:
8	chr15:42358545..42359423-chr15:42377294..42378091,3	MCF-7	breast:
9	chr15:42358352..42359263-chr15:42441667..42442628,3	MCF-7	breast:
10	chr15:42358267..42359328-chr15:42376085..42377139,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000159337	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10775125	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11629776	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11632871	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11633219	0.89[ASN][1000 genomes]
rs11633296	0.89[ASN][1000 genomes]
rs11635685	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11638531	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11638728	0.90[ASW][hapmap];0.87[YRI][hapmap]
rs12902878	0.90[CHB][hapmap];0.95[CHD][hapmap];0.94[LWK][hapmap];0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12906047	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs12906547	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1517555	0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17690138	0.93[ASN][1000 genomes]
rs2122674	0.91[ASN][1000 genomes]
rs2412657	0.81[CHB][hapmap];0.86[CHD][hapmap]
rs2840153	0.93[ASN][1000 genomes]
rs4924612	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4924618	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8031547	0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs938748	0.96[AFR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv1043641	chr15:42336584-42381240	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv904131	chr15:42343794-42390223	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv904132	chr15:42343794-42398046	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11070359	CHAC1	cis	cerebellum	SCAN
rs11070359	MFAP1	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42350400-42362600	Weak transcription	Gastric	stomach
2	chr15:42353800-42358600	Weak transcription	Liver	Liver
3	chr15:42356400-42359200	Enhancers	Fetal Muscle Leg	muscle
4	chr15:42356800-42358600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:42356800-42358800	Enhancers	HSMM	muscle
6	chr15:42356800-42359000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:42357000-42359200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:42357200-42358600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:42357200-42358600	Enhancers	HUVEC	blood vessel
10	chr15:42357200-42358800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:42357200-42358800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:42357200-42359000	Enhancers	Brain Germinal Matrix	brain
13	chr15:42357200-42359200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:42357200-42359200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr15:42357200-42359200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr15:42357200-42359400	Flanking Active TSS	HepG2	liver
17	chr15:42357400-42358600	Weak transcription	Brain Substantia Nigra	brain
18	chr15:42357600-42358600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:42357600-42358600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr15:42357600-42358800	Bivalent Enhancer	Adipose Nuclei	Adipose
21	chr15:42357800-42359000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:42358000-42360600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:42358200-42358600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr15:42358200-42358800	Enhancers	Hela-S3	cervix
25	chr15:42358200-42359200	Enhancers	Fetal Intestine Large	intestine
26	chr15:42358200-42359200	Enhancers	HMEC	breast
27	chr15:42358200-42360400	Weak transcription	HSMMtube	muscle
28	chr15:42358200-42363000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr15:42358400-42358800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:42358400-42358800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr15:42358400-42358800	Enhancers	Stomach Mucosa	stomach
32	chr15:42358400-42358800	Enhancers	NHEK	skin
33	chr15:42358400-42359000	Enhancers	Brain Cingulate Gyrus	brain
34	chr15:42358400-42359000	Enhancers	Esophagus	oesophagus
35	chr15:42358400-42359200	Enhancers	Pancreas	Pancrea
36	chr15:42358400-42359200	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr15:42358400-42359200	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr15:42358400-42361600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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