Variant report

Variant	rs212759
Chromosome Location	chr2:32426822-32426823
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPAST-1	chr2:32426669-32429068	NONHSAT069969

Extended variants
information (count: 91 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10172468	0.85[CHB][hapmap]
rs10490360	1.00[CEU][hapmap]
rs11124274	0.95[CEU][hapmap];0.85[TSI][hapmap]
rs11124275	1.00[CEU][hapmap]
rs11676938	0.95[CEU][hapmap];0.82[TSI][hapmap]
rs11678119	0.84[CEU][hapmap]
rs12614686	0.84[CEU][hapmap]
rs12989936	0.95[CEU][hapmap]
rs13017189	1.00[CEU][hapmap]
rs13022197	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs177083	0.80[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs17767988	1.00[CEU][hapmap]
rs212679	0.95[CEU][hapmap]
rs212694	0.94[ASN][1000 genomes]
rs212695	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs212698	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs212699	0.94[ASW][hapmap];0.94[CEU][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs212700	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs212701	0.94[ASW][hapmap];0.94[CEU][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs212704	0.87[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs212706	0.84[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.81[ASN][1000 genomes]
rs212707	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs212708	0.87[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs212713	0.89[CHD][hapmap];0.95[JPT][hapmap]
rs212714	0.87[ASW][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.80[AMR][1000 genomes]
rs212715	0.94[CEU][hapmap]
rs212716	0.89[CEU][hapmap]
rs212717	0.94[CEU][hapmap]
rs212721	0.87[ASW][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs212722	0.84[AMR][1000 genomes]
rs212723	0.84[AMR][1000 genomes]
rs212724	0.94[CEU][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs212725	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs212726	0.94[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes]
rs212727	1.00[ASW][hapmap];0.94[CEU][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.84[AMR][1000 genomes]
rs212728	0.82[AMR][1000 genomes]
rs212730	1.00[ASW][hapmap];0.94[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs212731	1.00[ASW][hapmap];0.94[CEU][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.83[AMR][1000 genomes]
rs212733	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs212734	0.80[AMR][1000 genomes]
rs212735	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs212736	0.82[YRI][hapmap]
rs212737	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs212739	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs212745	1.00[CEU][hapmap]
rs212746	1.00[CEU][hapmap]
rs212752	0.97[ASN][1000 genomes]
rs212756	0.97[ASN][1000 genomes]
rs212757	0.97[ASN][1000 genomes]
rs212758	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs212760	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs212762	0.81[CHB][hapmap]
rs2280967	1.00[CEU][hapmap]
rs2365555	1.00[CEU][hapmap];0.81[GIH][hapmap]
rs3752916	0.84[CEU][hapmap];0.82[YRI][hapmap]
rs3769602	0.84[CEU][hapmap]
rs3769604	0.95[CEU][hapmap]
rs3769606	0.95[CEU][hapmap];0.81[LWK][hapmap];0.82[TSI][hapmap]
rs3851310	0.89[CEU][hapmap]
rs430759	0.94[ASW][hapmap];0.94[CEU][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs435572	0.84[CEU][hapmap];0.83[YRI][hapmap]
rs443609	0.89[CEU][hapmap]
rs455060	1.00[ASW][hapmap];0.94[CEU][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs469305	0.85[CEU][hapmap]
rs479333	0.89[CEU][hapmap];0.83[GIH][hapmap];0.81[LWK][hapmap];0.83[YRI][hapmap]
rs494569	0.84[AMR][1000 genomes]
rs4952248	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs4952250	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs659239	0.89[CEU][hapmap];0.83[YRI][hapmap]
rs6723154	0.84[CEU][hapmap]
rs6725184	1.00[CEU][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs6737500	0.89[CEU][hapmap]
rs6748621	0.89[CEU][hapmap];0.82[GIH][hapmap]
rs6758024	1.00[CEU][hapmap]
rs6760105	1.00[CEU][hapmap]
rs7561519	0.95[CEU][hapmap]
rs7566162	0.95[CEU][hapmap]
rs7572964	0.84[CEU][hapmap]
rs7573543	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs7577696	1.00[CEU][hapmap]
rs7581340	0.90[CEU][hapmap];0.82[YRI][hapmap]
rs7586448	0.95[CEU][hapmap]
rs7601267	0.95[CEU][hapmap]
rs7605242	0.95[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv833670	chr2:32295778-32481857	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv817386	chr2:32332893-32724794	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1001038	chr2:32333378-32657112	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009359	chr2:32333378-32725117	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv535613	chr2:32333378-32725117	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	esv2422335	chr2:32412330-33200581	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs212759	DPY30	cis	parietal	SCAN
rs212759	SLC30A6	cis	cerebellum	SCAN
rs212759	EHD3	cis	parietal	SCAN
rs212759	NLRC4	cis	Lymphoblastoid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32391600-32452800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:32391800-32431400	Weak transcription	Stomach Mucosa	stomach
3	chr2:32391800-32453800	Weak transcription	Colonic Mucosa	Colon
4	chr2:32392000-32435800	Weak transcription	NHLF	lung
5	chr2:32392200-32445200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:32392800-32447600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:32399200-32449600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:32403000-32452200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:32404200-32445200	Weak transcription	Brain Angular Gyrus	brain
10	chr2:32404200-32447600	Weak transcription	Pancreas	Pancrea
11	chr2:32404200-32448000	Weak transcription	Colon Smooth Muscle	Colon
12	chr2:32404200-32452400	Weak transcription	Right Ventricle	heart
13	chr2:32404200-32460600	Weak transcription	Esophagus	oesophagus
14	chr2:32404400-32427800	Weak transcription	Aorta	Aorta
15	chr2:32404400-32447400	Weak transcription	HUVEC	blood vessel
16	chr2:32404400-32450800	Weak transcription	Gastric	stomach
17	chr2:32404800-32434000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr2:32404800-32447800	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:32408000-32428000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:32408000-32435800	Weak transcription	Psoas Muscle	Psoas
21	chr2:32410400-32436000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:32410400-32445200	Weak transcription	Fetal Kidney	kidney
23	chr2:32410600-32445200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr2:32411400-32445400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:32411600-32447800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:32412000-32450400	Weak transcription	Spleen	Spleen
27	chr2:32412200-32444200	Weak transcription	Fetal Brain Female	brain
28	chr2:32412800-32445200	Weak transcription	Brain Substantia Nigra	brain
29	chr2:32413200-32433600	Weak transcription	Fetal Lung	lung
30	chr2:32415200-32445200	Weak transcription	HMEC	breast
31	chr2:32415600-32432400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:32416000-32427600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:32416400-32427600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:32416600-32428600	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr2:32416800-32428400	Strong transcription	Fetal Intestine Large	intestine
36	chr2:32417200-32427400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:32417400-32427200	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr2:32417400-32427600	Strong transcription	Liver	Liver
39	chr2:32417400-32431000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:32418600-32427000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:32419200-32427000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr2:32419200-32446800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr2:32419800-32434000	Weak transcription	NHDF-Ad	bronchial
44	chr2:32419800-32445200	Weak transcription	HSMM	muscle
45	chr2:32420200-32432400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:32420600-32427600	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr2:32420600-32430200	Strong transcription	Fetal Thymus	thymus
48	chr2:32420800-32427000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:32420800-32428600	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr2:32420800-32447000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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