Variant report

Variant	rs17041797
Chromosome Location	chr2:111792193-111792194
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:111789979..111793920-chr2:111796275..111799559,5	MCF-7	breast:
2	chr2:111785222..111792269-chr2:111873385..111881089,20	MCF-7	breast:
3	chr2:111790430..111792678-chr2:111804599..111806279,2	MCF-7	breast:
4	chr2:111790298..111793489-chr2:111807175..111809652,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153094	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1384791	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1384794	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17041796	0.82[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3789083	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3827542	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55833189	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56105404	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56170128	0.84[EUR][1000 genomes]
rs59486976	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61145952	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66504720	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66509834	0.89[EUR][1000 genomes]
rs67234811	0.89[EUR][1000 genomes]
rs67250604	0.89[EUR][1000 genomes]
rs6730256	0.89[EUR][1000 genomes]
rs6738187	1.00[CEU][hapmap]
rs68080118	0.89[EUR][1000 genomes]
rs72834562	0.89[EUR][1000 genomes]
rs72834571	0.89[EUR][1000 genomes]
rs72834576	0.89[EUR][1000 genomes]
rs72834578	0.89[EUR][1000 genomes]
rs72834584	0.89[EUR][1000 genomes]
rs72834594	0.89[EUR][1000 genomes]
rs72834595	0.89[EUR][1000 genomes]
rs72946240	0.89[EUR][1000 genomes]
rs7420839	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][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	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874839	chr2:111400934-111868010	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17041797	RANBP2	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111786000-111795800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr2:111786200-111792400	Enhancers	Fetal Lung	lung
3	chr2:111786800-111792800	Enhancers	Fetal Intestine Small	intestine
4	chr2:111787000-111792800	Enhancers	Fetal Intestine Large	intestine
5	chr2:111787400-111795600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr2:111787800-111825400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:111788200-111792600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:111788200-111793400	Weak transcription	Fetal Thymus	thymus
9	chr2:111788200-111799200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:111790200-111792400	Enhancers	Fetal Heart	heart
11	chr2:111790800-111793600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:111790800-111799200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:111790800-111800200	Weak transcription	Spleen	Spleen
14	chr2:111791200-111792400	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr2:111791200-111792400	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr2:111791200-111792600	Enhancers	Duodenum Mucosa	Duodenum
17	chr2:111791200-111794600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:111791200-111795600	Weak transcription	Gastric	stomach
19	chr2:111791200-111795800	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr2:111791400-111792400	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr2:111791400-111793400	Weak transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links