Variant report

Variant	rs1905291
Chromosome Location	chr2:142277783-142277784
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	chr2:142265220..142267079-chr2:142275773..142278354,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10496881	0.85[JPT][hapmap]
rs11887304	0.85[JPT][hapmap]
rs13019402	0.82[YRI][hapmap]
rs13419140	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1483144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846216	0.85[JPT][hapmap]
rs16846224	0.82[JPT][hapmap]
rs16846251	0.85[JPT][hapmap]
rs16846274	0.85[JPT][hapmap]
rs16846416	0.85[JPT][hapmap];0.88[MEX][hapmap]
rs16846509	0.85[JPT][hapmap]
rs16846539	0.85[JPT][hapmap]
rs16855055	0.85[JPT][hapmap]
rs34962994	0.82[EUR][1000 genomes]
rs41396347	0.85[JPT][hapmap]
rs4408668	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4491668	0.85[JPT][hapmap]
rs4547471	0.85[JPT][hapmap]
rs4560051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4575660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4954914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4954915	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55869530	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6429898	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6749551	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9287319	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817518	chr2:141714174-142287302	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv583203	chr2:142055133-142378975	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv875240	chr2:142199421-142347455	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
4	nsv470491	chr2:142254119-142299923	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
5	nsv834393	chr2:142256714-142431564	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
6	nsv583210	chr2:142259592-142295042	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv459629	chr2:142263400-142295042	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv583211	chr2:142263400-142295042	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	nsv583212	chr2:142263979-142309330	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1905291	SLIT2	trans	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142277000-142277800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:142277200-142277800	Enhancers	Brain Hippocampus Middle	brain
3	chr2:142277200-142279000	Enhancers	Brain Angular Gyrus	brain
4	chr2:142277200-142279000	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr2:142277400-142278200	Enhancers	Brain Anterior Caudate	brain
6	chr2:142277400-142278200	Enhancers	Brain Cingulate Gyrus	brain
7	chr2:142277600-142278000	Enhancers	Brain Substantia Nigra	brain
8	chr2:142277600-142278400	Enhancers	HUES64 Cell Line	embryonic stem cell

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