Variant report

Variant	rs1577619
Chromosome Location	chr6:142276494-142276495
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1006257	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1007718	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10457728	1.00[ASN][1000 genomes]
rs12191856	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192083	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197645	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12199467	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204765	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1336263	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1336268	1.00[ASN][1000 genomes]
rs1575871	1.00[ASN][1000 genomes]
rs2784946	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2842764	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56893373	1.00[ASN][1000 genomes]
rs56954968	1.00[ASN][1000 genomes]
rs59341481	1.00[ASN][1000 genomes]
rs62431978	1.00[ASN][1000 genomes]
rs62432010	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760213	1.00[ASN][1000 genomes]
rs9484567	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830823	chr6:142111420-142305417	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1029504	chr6:142131846-142333198	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv538458	chr6:142131846-142333198	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1017195	chr6:142142454-142336722	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv886729	chr6:142192725-142277769	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv604792	chr6:142192725-142399251	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv464067	chr6:142214093-142283198	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv604793	chr6:142214093-142283198	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv886730	chr6:142214093-142299345	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1019170	chr6:142234933-142397088	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv464068	chr6:142263201-142316177	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1577619	STX11	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142274600-142276800	Weak transcription	Liver	Liver
2	chr6:142274800-142284000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:142275400-142277200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:142275400-142278000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:142276000-142276600	Weak transcription	Aorta	Aorta
6	chr6:142276000-142277200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:142276000-142277800	Enhancers	Stomach Smooth Muscle	stomach
8	chr6:142276200-142277200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:142276200-142277800	Enhancers	Ovary	ovary
10	chr6:142276400-142276600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:142276400-142276800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:142276400-142277200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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