Variant report

Variant	rs532318
Chromosome Location	chr11:58690549-58690550
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	chr11:58690547-58691196	HCT-116	colon:	n/a	n/a
2	CTCF	chr11:58690100-58691258	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr11:58690446-58691302	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr11:58690540-58691213	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr11:58690420-58690570	GM12864	blood:	n/a	n/a
6	RAD21	chr11:58690522-58691166	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
GLYATL1	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11229690	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229707	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11603726	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1788552	0.83[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1892866	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1938785	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1938787	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1938788	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2005121	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2105736	0.95[ASN][1000 genomes]
rs2156322	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs474121	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs478587	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs478705	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs480196	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs482219	0.82[CHD][hapmap]
rs482751	0.87[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs483991	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs486507	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs488446	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs489782	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs489846	0.94[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs501703	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs510360	0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs513677	0.85[ASN][1000 genomes]
rs516803	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs530481	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs533087	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs535218	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs538472	0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs544687	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs546051	0.88[ASN][1000 genomes]
rs550864	0.88[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs563370	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs564335	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs573271	0.81[JPT][hapmap]
rs574058	0.90[ASN][1000 genomes]
rs576790	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7120597	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv3444895	chr11:58614102-58779384	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription 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
4	esv3445007	chr11:58638330-58709867	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv3502182	chr11:58668199-58731237	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3502181	chr11:58668236-58731215	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3478019	chr11:58668282-58731214	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3478030	chr11:58668282-58731214	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv3502183	chr11:58668353-58731177	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv3393019	chr11:58679419-58880845	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs532318	OR9G1	cis	cerebellum	SCAN
rs532318	C11orf10	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58686200-58692600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr11:58687200-58690600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr11:58687200-58694800	Enhancers	Fetal Intestine Large	intestine
4	chr11:58687200-58694800	Enhancers	Fetal Intestine Small	intestine
5	chr11:58687400-58691200	Enhancers	Fetal Kidney	kidney
6	chr11:58687600-58690600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr11:58687600-58690600	Weak transcription	HSMM	muscle
8	chr11:58687600-58690600	Weak transcription	NH-A	brain
9	chr11:58687600-58690800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr11:58687800-58690600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr11:58687800-58690600	Weak transcription	HMEC	breast
12	chr11:58687800-58690800	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr11:58688000-58690600	Weak transcription	Fetal Thymus	thymus
14	chr11:58689000-58690600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr11:58689200-58691200	Enhancers	Colonic Mucosa	Colon
16	chr11:58689600-58694800	Weak transcription	Esophagus	oesophagus
17	chr11:58690000-58690600	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr11:58690000-58690600	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr11:58690000-58690600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr11:58690000-58690800	Enhancers	H1 Cell Line	embryonic stem cell
21	chr11:58690000-58690800	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr11:58690000-58691800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr11:58690200-58690600	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr11:58690200-58691000	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr11:58690400-58690600	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr11:58690400-58690600	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr11:58690400-58690600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr11:58690400-58690800	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr11:58690400-58690800	Enhancers	H9 Cell Line	embryonic stem cell
30	chr11:58690400-58690800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr11:58690400-58690800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr11:58690400-58690800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr11:58690400-58690800	Enhancers	NHEK	skin
34	chr11:58690400-58691000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr11:58690400-58691200	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr11:58690400-58691200	Enhancers	Thymus	Thymus
37	chr11:58690400-58693400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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