Variant report

Variant	rs659857
Chromosome Location	chr11:65629932-65629933
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10791828	0.84[AMR][1000 genomes]
rs10896053	0.88[GIH][hapmap]
rs11227311	0.84[GIH][hapmap]
rs1204772	0.88[GIH][hapmap]
rs12575663	0.80[GIH][hapmap]
rs13817	0.93[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1939212	0.92[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4621	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs508548	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs538394	0.96[CEU][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs545500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs558114	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570387	0.80[GIH][hapmap]
rs601887	0.88[GIH][hapmap]
rs621348	0.88[GIH][hapmap]
rs630303	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630755	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs633800	0.80[GIH][hapmap]
rs633877	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs635375	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648732	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs652021	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs656040	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659824	0.80[GIH][hapmap];0.86[MKK][hapmap]
rs665306	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs667555	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs668356	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs679147	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7107912	0.84[GIH][hapmap]
rs7114014	0.92[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap]
rs7114237	0.88[GIH][hapmap]
rs7125986	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7947741	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7947929	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
2	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
3	esv2758274	chr11:65559893-65722363	Genic enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	esv2759834	chr11:65559893-65722363	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv427890	chr11:65559893-65722363	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv897761	chr11:65580638-65738566	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	186 gene(s)	inside rSNPs	diseases
7	nsv555215	chr11:65581579-65676516	Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
8	nsv897762	chr11:65613218-65758854	Active TSS Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
9	nsv897763	chr11:65613348-65644027	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	121 gene(s)	inside rSNPs	diseases
10	nsv897764	chr11:65613348-65695222	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
11	nsv897765	chr11:65623708-65758854	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
12	nsv897766	chr11:65624025-65644027	Transcr. at gene 5' and 3' Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs659857	PACS1	cis	parietal	SCAN
rs659857	FIBP	Cis_1M	lymphoblastoid	RTeQTL
rs659857	EIF1AD	cis	parietal	SCAN
rs659857	SNX32	cis	parietal	SCAN
rs659857	PLCB3	cis	parietal	SCAN
rs659857	SNX32	cis	Thyroid	GTEx
rs659857	SNX32	cis	cerebellum	SCAN
rs659857	SNX32	cis	Artery Tibial	GTEx
rs659857	SNX32	cis	Esophagus Muscularis	GTEx
rs659857	FIBP	cis	cerebellum	SCAN
rs659857	SNX32	cis	Whole Blood	GTEx
rs659857	CARNS1	cis	cerebellum	SCAN
rs659857	RAB3IL1	cis	cerebellum	SCAN
rs659857	SNORD31	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65628200-65633600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr11:65628800-65639600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr11:65629000-65630000	Genic enhancers	Primary B cells from peripheral blood	blood
4	chr11:65629000-65630000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr11:65629000-65630600	Genic enhancers	Brain Hippocampus Middle	brain
6	chr11:65629000-65630600	Enhancers	Fetal Brain Male	brain
7	chr11:65629000-65631000	Genic enhancers	Fetal Thymus	thymus
8	chr11:65629000-65631600	Genic enhancers	Spleen	Spleen
9	chr11:65629000-65632600	Genic enhancers	Primary T cells fromperipheralblood	blood
10	chr11:65629000-65639600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr11:65629200-65630000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
12	chr11:65629200-65630000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr11:65629200-65630000	Genic enhancers	Placenta	Placenta
14	chr11:65629200-65630000	Genic enhancers	Gastric	stomach
15	chr11:65629200-65630000	Genic enhancers	Lung	lung
16	chr11:65629200-65630000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
17	chr11:65629200-65630000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
18	chr11:65629200-65630200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr11:65629200-65630200	Genic enhancers	Monocytes-CD14+_RO01746	blood
20	chr11:65629200-65630400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr11:65629200-65630400	Genic enhancers	Brain Cingulate Gyrus	brain
22	chr11:65629200-65630400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr11:65629200-65630600	Genic enhancers	Pancreas	Pancrea
24	chr11:65629200-65630600	Enhancers	Stomach Mucosa	stomach
25	chr11:65629200-65630800	Genic enhancers	Colon Smooth Muscle	Colon
26	chr11:65629200-65631000	Genic enhancers	Adipose Nuclei	Adipose
27	chr11:65629200-65631000	Genic enhancers	Brain Inferior Temporal Lobe	brain
28	chr11:65629200-65631200	Genic enhancers	Right Ventricle	heart
29	chr11:65629200-65631600	Genic enhancers	Fetal Stomach	stomach
30	chr11:65629200-65632800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
31	chr11:65629200-65634600	Strong transcription	Aorta	Aorta
32	chr11:65629400-65630000	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr11:65629400-65630000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr11:65629400-65630000	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr11:65629400-65630000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr11:65629400-65630000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr11:65629400-65630000	Genic enhancers	Fetal Intestine Large	intestine
38	chr11:65629400-65630000	Genic enhancers	Fetal Intestine Small	intestine
39	chr11:65629400-65630000	Enhancers	HSMMtube	muscle
40	chr11:65629400-65630000	Enhancers	NHDF-Ad	bronchial
41	chr11:65629400-65630400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
42	chr11:65629400-65630400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
43	chr11:65629400-65630400	Genic enhancers	Fetal Muscle Leg	muscle
44	chr11:65629400-65630400	Genic enhancers	Rectal Mucosa Donor 31	rectum
45	chr11:65629400-65630600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
46	chr11:65629400-65630600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
47	chr11:65629400-65631000	Genic enhancers	Duodenum Smooth Muscle	Duodenum
48	chr11:65629400-65631000	Weak transcription	Small Intestine	intestine
49	chr11:65629400-65631200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr11:65629400-65631600	Weak transcription	Fetal Kidney	kidney

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