Variant report

Variant	rs6049775
Chromosome Location	chr20:24526724-24526725
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs13041310	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1555892	0.89[CEU][hapmap];0.88[LWK][hapmap];0.82[MEX][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2386954	0.80[CEU][hapmap]
rs2386956	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4283490	0.84[AMR][1000 genomes]
rs6036832	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6049755	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6049757	1.00[CEU][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6049758	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6049759	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6049760	1.00[CEU][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6049765	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6049768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6049771	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6076233	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6076235	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6114752	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6114757	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6114760	0.82[EUR][1000 genomes]
rs6114768	0.89[ASW][hapmap];0.85[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6132742	0.89[ASW][hapmap];0.89[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6132743	0.89[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6132744	0.85[ASN][1000 genomes]
rs6138316	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6138318	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6138319	0.88[ASN][1000 genomes]
rs715863	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1058146	chr20:24210196-24531087	Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6049775	CST9	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24517200-24526800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr20:24521200-24528400	Weak transcription	HMEC	breast
3	chr20:24522400-24526800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr20:24522800-24528400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr20:24523000-24528200	Weak transcription	Brain Anterior Caudate	brain
6	chr20:24523400-24527600	Weak transcription	Fetal Brain Female	brain
7	chr20:24523600-24526800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr20:24523600-24530800	Weak transcription	Fetal Heart	heart
9	chr20:24523800-24528800	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr20:24523800-24528800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr20:24524200-24526800	Strong transcription	Brain Angular Gyrus	brain
12	chr20:24525000-24527000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr20:24525000-24527000	Strong transcription	Brain Hippocampus Middle	brain
14	chr20:24525000-24528600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr20:24525400-24541800	Weak transcription	Left Ventricle	heart
16	chr20:24526200-24527000	Weak transcription	Right Ventricle	heart
17	chr20:24526600-24527400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
18	chr20:24526600-24527400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr20:24526600-24527400	ZNF genes & repeats	Brain Cingulate Gyrus	brain
20	chr20:24526600-24527400	ZNF genes & repeats	Brain Substantia Nigra	brain
21	chr20:24526600-24527400	ZNF genes & repeats	Fetal Muscle Leg	muscle
22	chr20:24526600-24529400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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