Variant report

Variant	rs10461245
Chromosome Location	chr4:158924505-158924506
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	chr4:158923730..158926268-chr4:158927220..158929131,2	MCF-7	breast:
2	chr4:158921420..158925394-chr4:158925624..158927441,3	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10008208	0.86[CEU][hapmap];0.82[CHB][hapmap]
rs10012339	0.92[CEU][hapmap]
rs10028490	0.93[CEU][hapmap];0.82[CHB][hapmap]
rs10461268	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10461269	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731973	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12645131	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs12648410	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs14202	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs17036927	1.00[JPT][hapmap]
rs2346321	0.86[CEU][hapmap]
rs2881373	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs35025809	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4234917	0.93[CEU][hapmap]
rs4317248	0.93[CEU][hapmap]
rs4345228	0.93[CEU][hapmap];0.82[CHB][hapmap]
rs4389619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4457000	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4501266	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs4691455	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs4691461	0.86[CEU][hapmap];0.82[CHB][hapmap]
rs6536292	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6536299	0.93[CEU][hapmap];0.82[CHB][hapmap]
rs6820988	0.82[CHB][hapmap]
rs6830702	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs6833198	0.86[CEU][hapmap];0.82[CHB][hapmap]
rs7437833	0.85[AFR][1000 genomes]
rs7657303	0.91[MKK][hapmap]
rs8370	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs9991405	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv881288	chr4:158891733-159028080	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10461245	PRSS12	trans	cerebellum	SCAN
rs10461245	FAM198B	cis	Whole Blood	GTEx
rs10461245	FAM198B	cis	parietal	SCAN
rs10461245	RP11-597D13.9	cis	Skin Sun Exposed Lower leg	GTEx
rs10461245	RP11-597D13.7	cis	Heart Left Ventricle	GTEx
rs10461245	TMEM144	cis	Esophagus Muscularis	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:158913800-158928200	Weak transcription	HSMM	muscle
2	chr4:158913800-158930000	Weak transcription	Right Atrium	heart
3	chr4:158917800-158926400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:158922600-158930000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr4:158922800-158926000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr4:158922800-158929200	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr4:158923000-158924600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr4:158923200-158928400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:158923600-158925600	Weak transcription	Colon Smooth Muscle	Colon
10	chr4:158923600-158927800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:158923800-158926200	Weak transcription	Fetal Heart	heart
12	chr4:158923800-158926600	Weak transcription	HUVEC	blood vessel
13	chr4:158923800-158929800	Weak transcription	Left Ventricle	heart
14	chr4:158923800-158939400	Weak transcription	HepG2	liver
15	chr4:158924000-158924800	Enhancers	Primary hematopoietic stem cells	blood
16	chr4:158924000-158925200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:158924200-158925400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr4:158924400-158924800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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