Variant report

Variant	rs10176475
Chromosome Location	chr2:178976514-178976515
allele	C/T
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	chr2:178976500-178976650	GM12871	blood:	n/a	n/a
2	CTCF	chr2:178976460-178976610	Caco-2	colon:	n/a	n/a
3	CTCF	chr2:178976400-178976550	GM12865	blood:	n/a	n/a
4	CTCF	chr2:178976420-178976570	HRPEpiC	eye:	n/a	n/a
5	CEBPB	chr2:178976441-178977526	HCT-116	colon:	n/a	chr2:178977004-178977013 chr2:178977002-178977015 chr2:178977002-178977013
6	CTCF	chr2:178976252-178977766	A549	lung:	n/a	chr2:178977085-178977095 chr2:178977083-178977096 chr2:178977081-178977097 chr2:178977080-178977098

No.	Distal block	Cell Line	Cell type
1	chr2:178970656..178974678-chr2:178975520..178979270,3	K562	blood:
2	chr2:178974133..178981122-chr2:179276785..179281060,9	K562	blood:
3	chr2:178975231..178977429-chr2:179315218..179317152,2	MCF-7	breast:
4	chr2:178975761..178978600-chr2:179056476..179059620,3	K562	blood:
5	chr2:178975067..178978289-chr2:179058254..179060575,4	MCF-7	breast:
6	chr2:178974707..178979925-chr2:179277151..179280371,6	K562	blood:
7	chr2:178972756..178975132-chr2:178975866..178978416,2	MCF-7	breast:
8	chr2:178976079..178979038-chr2:178986555..178992721,6	MCF-7	breast:
9	chr2:178976419..178978821-chr2:179313368..179316809,4	K562	blood:

Variant related genes	Relation type
PDE11A	TF binding region
RBM45	TF binding region
ENSG00000180228	Chromatin interaction
ENSG00000204311	Chromatin interaction
ENSG00000155636	Chromatin interaction
ENSG00000079156	Chromatin interaction
ENSG00000128655	Chromatin interaction
ENSG00000223960	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10198111	0.88[CHB][hapmap]
rs10432485	0.94[JPT][hapmap]
rs11674668	0.82[CHB][hapmap]
rs11886139	0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11887974	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11899905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13408924	0.89[ASW][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1347441	0.88[CHB][hapmap]
rs1369515	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1369517	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1435571	0.93[CEU][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap]
rs1852502	0.82[CHD][hapmap]
rs2034255	0.93[ASN][1000 genomes]
rs2043547	0.82[CHB][hapmap]
rs2163647	0.94[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2217838	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4300869	0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs56103916	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6433709	0.88[CHB][hapmap]
rs6709256	0.82[CHB][hapmap]
rs6709343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6710329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6714047	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6740828	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6754705	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs736842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7583491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7608073	0.82[CHB][hapmap]
rs9288014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv583739	chr2:178942302-178993562	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv518790	chr2:178963445-179000291	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv875452	chr2:178963445-179167766	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10176475	AGPS	cis	lymphoblastoid	seeQTL
rs10176475	PLEKHA3	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178971200-178976800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:178973200-178977000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:178975600-178976600	Enhancers	NHEK	skin
4	chr2:178976400-178976600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:178976400-178976600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:178976400-178976600	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr2:178976400-178976600	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr2:178976400-178976600	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr2:178976400-178976600	Enhancers	Dnd41	blood
10	chr2:178976400-178976800	Enhancers	Primary T cells from cord blood	blood
11	chr2:178976400-178976800	Enhancers	Primary T cells fromperipheralblood	blood
12	chr2:178976400-178976800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:178976400-178976800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:178976400-178976800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr2:178976400-178976800	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr2:178976400-178976800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:178976400-178976800	Enhancers	Placenta	Placenta
18	chr2:178976400-178976800	Enhancers	Hela-S3	cervix
19	chr2:178976400-178976800	Enhancers	HMEC	breast
20	chr2:178976400-178977000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links