Variant report

Variant	rs16823254
Chromosome Location	chr2:183309282-183309283
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10207132	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10497598	0.94[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs10497600	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10497601	0.91[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs10497602	0.81[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10497603	1.00[YRI][hapmap]
rs1125184	1.00[ASW][hapmap];0.84[LWK][hapmap];0.83[AFR][1000 genomes]
rs11686025	0.88[CEU][hapmap]
rs12465662	1.00[ASW][hapmap];0.84[LWK][hapmap]
rs12466618	1.00[YRI][hapmap]
rs12468232	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs12468346	1.00[YRI][hapmap]
rs12473820	0.91[AFR][1000 genomes]
rs12478132	1.00[YRI][hapmap]
rs12479259	1.00[YRI][hapmap]
rs13407156	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1346775	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs1367203	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1430147	0.94[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs1430148	0.94[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs1583114	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16823233	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16823257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17265027	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17265061	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17265189	1.00[YRI][hapmap]
rs17356152	0.85[CEU][hapmap];0.81[MEX][hapmap]
rs17356166	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17356207	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17356214	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17356296	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs17356303	1.00[YRI][hapmap]
rs1946815	0.85[CEU][hapmap];0.81[MEX][hapmap]
rs28569979	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34103461	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35809203	0.83[AFR][1000 genomes]
rs4091077	0.85[JPT][hapmap]
rs4318355	0.90[AFR][1000 genomes]
rs4496292	1.00[YRI][hapmap]
rs4666837	1.00[YRI][hapmap]
rs62188260	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62188266	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62188267	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62188268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62188269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62188270	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62188283	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62188284	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62188286	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62188287	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62188288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62188289	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62188290	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62188295	0.83[AFR][1000 genomes]
rs62190201	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62190677	0.81[AFR][1000 genomes]
rs6760364	1.00[YRI][hapmap];0.87[AFR][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	nsv533782	chr2:183059730-183500040	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv834481	chr2:183189758-183339577	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	esv2830429	chr2:183300759-183545378	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16823254	SSFA2	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183298800-183320800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:183301400-183309800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:183307200-183309800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:183308400-183311000	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:183308400-183312000	Weak transcription	Left Ventricle	heart
6	chr2:183308800-183310600	Enhancers	HSMMtube	muscle
7	chr2:183309000-183311400	Enhancers	HSMM	muscle
8	chr2:183309200-183309800	Enhancers	Muscle Satellite Cultured Cells	--
9	chr2:183309200-183311200	Enhancers	Hela-S3	cervix
10	chr2:183309200-183311400	Enhancers	Osteobl	bone
11	chr2:183309200-183313800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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