Variant report

Variant	rs2158005
Chromosome Location	chr17:59786535-59786536
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:59488477..59493840-chr17:59781559..59787606,7	MCF-7	breast:
2	chr17:59784025..59787168-chr17:59909031..59912201,3	MCF-7	breast:
3	chr17:59786284..59788670-chr17:59864199..59866919,2	MCF-7	breast:
4	chr16:89626744..89628368-chr17:59785949..59788832,2	MCF-7	breast:
5	chr17:59687653..59691207-chr17:59785132..59788535,3	MCF-7	breast:
6	chr17:59775949..59780769-chr17:59781104..59786917,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267280	Chromatin interaction
ENSG00000200084	Chromatin interaction
ENSG00000167526	Chromatin interaction
ENSG00000187013	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11079451	0.95[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs11079454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11654606	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11867566	0.83[ASN][1000 genomes]
rs11871785	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2007931	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2040609	0.91[CHB][hapmap]
rs2106663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2159451	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35090865	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35524448	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4988357	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56218811	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62071871	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62071872	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6504058	0.82[CHB][hapmap]
rs6504065	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67223644	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7214703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219555	0.86[ASN][1000 genomes]
rs7220740	0.86[ASN][1000 genomes]
rs7222482	0.95[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs8064683	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9908115	0.88[ASW][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap];0.86[ASN][1000 genomes]
rs9912366	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9915787	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][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	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv908673	chr17:59767501-59926645	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2158005	AKAP1	cis	cerebellum	SCAN
rs2158005	RNF43	cis	parietal	SCAN
rs2158005	VEZF1	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59763400-59792800	Weak transcription	NH-A	brain
2	chr17:59766000-59819000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr17:59767600-59792800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr17:59767600-59793200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr17:59771800-59794600	Weak transcription	HSMM	muscle
6	chr17:59778200-59805800	Weak transcription	Thymus	Thymus
7	chr17:59779400-59790000	Weak transcription	HepG2	liver
8	chr17:59780000-59793400	Weak transcription	Fetal Heart	heart
9	chr17:59780400-59791000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr17:59780800-59793000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr17:59781000-59791800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr17:59781600-59835400	Weak transcription	Hela-S3	cervix
13	chr17:59782800-59793200	Weak transcription	Fetal Lung	lung
14	chr17:59783000-59793600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr17:59783200-59790200	Weak transcription	A549	lung
16	chr17:59783400-59793200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr17:59783600-59787800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr17:59783800-59793600	Weak transcription	Fetal Intestine Large	intestine
19	chr17:59784000-59794600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr17:59784200-59793000	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr17:59784400-59792800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr17:59784400-59793400	Weak transcription	NHEK	skin
23	chr17:59784400-59815200	Weak transcription	HMEC	breast
24	chr17:59784600-59788600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr17:59784800-59787200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr17:59785000-59786600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr17:59785000-59787400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr17:59785000-59790400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr17:59785000-59793400	Weak transcription	K562	blood
30	chr17:59785200-59794400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr17:59785400-59786600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr17:59785600-59787000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr17:59785600-59787200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr17:59785600-59787200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr17:59785600-59788000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr17:59785600-59788800	Strong transcription	Primary hematopoietic stem cells	blood
37	chr17:59785600-59791600	Strong transcription	Dnd41	blood
38	chr17:59785800-59786600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr17:59786000-59786600	Strong transcription	Fetal Thymus	thymus
40	chr17:59786200-59786600	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr17:59786200-59790400	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr17:59786200-59790600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr17:59786400-59788000	Weak transcription	GM12878-XiMat	blood
44	chr17:59786400-59792800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr17:59786400-59793600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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