Variant report

Variant	rs2525096
Chromosome Location	chr17:46076965-46076966
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr17:46076960-46077110	BE2_C	brain:	n/a	n/a
2	FOS	chr17:46076928-46077236	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46047115..46050048-chr17:46075533..46077931,3	MCF-7	breast:
2	chr17:46075615..46077528-chr17:46123330..46125868,2	MCF-7	breast:
3	chr17:46066387..46068128-chr17:46076064..46078648,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264701	TF binding region
ENSG00000082641	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000108465	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11079804	0.88[CHB][hapmap]
rs11545723	0.94[CHB][hapmap];0.81[GIH][hapmap]
rs1476578	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1476579	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17617250	0.87[CHB][hapmap]
rs2003477	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2003478	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2255697	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2255815	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2525084	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2525085	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525087	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525088	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525090	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525091	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525092	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525093	1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525094	0.80[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525098	0.88[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2525103	0.86[TSI][hapmap]
rs2597161	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2597165	0.95[CEU][hapmap];0.88[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2597166	0.87[AFR][1000 genomes]
rs2597168	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2597171	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2597172	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2597173	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2597174	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2597179	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2597180	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2597181	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2875746	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2905845	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2905846	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2905848	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2905849	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2905850	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2905851	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2905852	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2905853	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34190379	0.91[ASN][1000 genomes]
rs35653190	0.86[ASN][1000 genomes]
rs4793734	0.94[CHB][hapmap];0.81[GIH][hapmap]
rs4794225	0.82[CHB][hapmap]
rs62064873	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6503949	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs729785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs729786	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs737130	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs739853	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7406338	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7503584	1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap];0.91[ASN][1000 genomes]
rs8076314	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs885634	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[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	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2525096	PNPO	cis	parietal	SCAN
rs2525096	PNPO	cis	cerebellum	SCAN
rs2525096	NFE2L1	cis	parietal	SCAN
rs2525096	ASB16	cis	parietal	SCAN
rs2525096	ETV4	cis	parietal	SCAN
rs2525096	C17orf57	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46061800-46079600	Weak transcription	Right Atrium	heart
2	chr17:46068000-46079800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr17:46069000-46077000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr17:46069000-46079600	Weak transcription	Fetal Thymus	thymus
5	chr17:46073200-46078800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr17:46073400-46077000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr17:46073400-46077000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr17:46073400-46081000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr17:46073800-46077000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr17:46073800-46077000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr17:46073800-46077000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr17:46073800-46077000	Weak transcription	Fetal Brain Female	brain
13	chr17:46073800-46078800	Weak transcription	Brain Germinal Matrix	brain
14	chr17:46073800-46079600	Weak transcription	Esophagus	oesophagus
15	chr17:46074000-46077000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr17:46074000-46077000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr17:46074200-46077000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr17:46074200-46078800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr17:46074200-46079600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr17:46074200-46079600	Weak transcription	K562	blood
21	chr17:46074200-46079800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr17:46074400-46077000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:46075400-46077000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr17:46075600-46077000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr17:46075600-46077000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr17:46075600-46077000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr17:46075600-46077000	Weak transcription	Placenta	Placenta
28	chr17:46075600-46077000	Weak transcription	HSMMtube	muscle
29	chr17:46075600-46079000	Weak transcription	Adipose Nuclei	Adipose
30	chr17:46075800-46077000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr17:46075800-46077000	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr17:46076400-46077400	Enhancers	HSMM	muscle
33	chr17:46076400-46077600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr17:46076400-46079400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr17:46076400-46084600	Enhancers	Fetal Brain Male	brain
36	chr17:46076600-46077800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr17:46076600-46077800	Enhancers	Muscle Satellite Cultured Cells	--
38	chr17:46076800-46077400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr17:46076800-46077600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr17:46076800-46077800	Enhancers	Osteobl	bone
41	chr17:46076800-46078000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr17:46076800-46078000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr17:46076800-46085600	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links