Variant report

Variant	rs4841339
Chromosome Location	chr8:10294330-10294331
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:10293147..10295471-chr8:10296811..10299239,2	K562	blood:
2	chr8:10290739..10292284-chr8:10294138..10295858,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MSRA-1	chr8:10291182-10295822	ENSG00000261451.1
2	lnc-MSRA-1	chr8:10293466-10295495	NONHSAT124987

Variant related genes	Relation type
ENSG00000261451	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11785972	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13248291	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13250363	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13265461	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13270515	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17184069	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34552276	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34950718	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35088325	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35324154	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35505217	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35742317	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35926643	0.81[EUR][1000 genomes]
rs4271011	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4446774	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4478621	1.00[CEU][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4538933	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4841348	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6601464	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6601479	0.88[GIH][hapmap]
rs6981847	0.88[GIH][hapmap]
rs6987165	0.88[GIH][hapmap]
rs6990962	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7014983	0.95[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71516574	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71516576	0.81[AMR][1000 genomes]
rs7815324	0.88[GIH][hapmap]
rs7842777	0.88[GIH][hapmap]
rs9650623	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030934	chr8:10065169-10561161	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv890347	chr8:10153082-10331636	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1022994	chr8:10190618-10660122	Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv539466	chr8:10190618-10660122	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv527326	chr8:10199548-10320019	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv1025557	chr8:10216726-10555187	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv917085	chr8:10237508-10828204	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv610266	chr8:10250758-10294330	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
9	nsv610267	chr8:10268736-10526742	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv890349	chr8:10294330-10355302	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4841339	PRSS55	cis	parietal	SCAN
rs4841339	PRSS55	cis	cerebellum	SCAN
rs4841339	FLJ10661	cis	cerebellum	SCAN
rs4841339	MFHAS1	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10282600-10295200	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr8:10283200-10295200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr8:10285800-10305200	Weak transcription	Lung	lung
4	chr8:10291400-10301200	Weak transcription	Pancreas	Pancrea
5	chr8:10292200-10294400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr8:10292200-10321400	Weak transcription	Fetal Brain Male	brain
7	chr8:10292400-10294400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr8:10293600-10294400	Strong transcription	Left Ventricle	heart
9	chr8:10293800-10294400	ZNF genes & repeats	Primary T cells from cord blood	blood
10	chr8:10294000-10296200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr8:10294000-10302400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr8:10294000-10304000	Weak transcription	Fetal Brain Female	brain
13	chr8:10294200-10302800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr8:10294200-10306600	Weak transcription	Liver	Liver

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