Variant report

Variant	rs10511298
Chromosome Location	chr3:111267564-111267565
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111264050..111266298-chr3:111267284..111269924,2	K562	blood:
2	chr3:111267159..111269503-chr3:111303920..111306362,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10934101	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11916952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12494356	0.83[ASN][1000 genomes]
rs13066911	0.85[ASN][1000 genomes]
rs1391356	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1391358	0.81[ASN][1000 genomes]
rs1497990	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1513323	0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1603687	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2088468	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2173318	0.81[GIH][hapmap]
rs2276873	0.88[CEU][hapmap];0.91[GIH][hapmap]
rs2399391	0.81[AFR][1000 genomes]
rs6764960	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6788797	0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs721336	0.85[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7616420	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7619086	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7628253	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7653347	0.88[CEU][hapmap];0.91[GIH][hapmap]
rs883113	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs924262	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs968910	0.86[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv997756	chr3:111226058-111376585	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv3946	chr3:111236035-111283038	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10511298	ZNF80	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111260200-111269800	Enhancers	Primary hematopoietic stem cells	blood
2	chr3:111262600-111268400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:111262600-111269400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
4	chr3:111263200-111269000	Transcr. at gene 5' and 3'	Dnd41	blood
5	chr3:111263200-111269200	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr3:111264200-111268800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:111264400-111268000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:111264600-111268400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:111265000-111271600	Enhancers	Primary B cells from peripheral blood	blood
10	chr3:111265800-111267600	Active TSS	Primary T cells fromperipheralblood	blood
11	chr3:111265800-111271600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr3:111266200-111267600	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr3:111266200-111267600	Flanking Active TSS	GM12878-XiMat	blood
14	chr3:111266200-111267600	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr3:111266200-111268200	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr3:111266200-111268200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr3:111266200-111268400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr3:111266200-111268800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr3:111266400-111268000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr3:111266600-111267600	Active TSS	Fetal Thymus	thymus
21	chr3:111266600-111268400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:111266800-111267800	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr3:111266800-111268000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
24	chr3:111266800-111268000	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr3:111266800-111268800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr3:111267000-111267600	Weak transcription	Small Intestine	intestine
27	chr3:111267000-111267800	Enhancers	H9 Cell Line	embryonic stem cell
28	chr3:111267000-111268400	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr3:111267000-111268600	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr3:111267200-111268000	Active TSS	Thymus	Thymus
31	chr3:111267200-111269800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:111267400-111267800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:111267400-111268000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:111267400-111268000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:111267400-111268000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:111267400-111268400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr3:111267400-111270200	Enhancers	Primary B cells from cord blood	blood
38	chr3:111267400-111271000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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