Variant report

Variant	rs13400121
Chromosome Location	chr2:142860912-142860913
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	chr2:142856831..142859163-chr2:142860211..142863049,2	MCF-7	breast:
2	chr2:142860532..142863086-chr2:142865572..142867375,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1001628	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1011861	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10179879	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10181071	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190320	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10201177	0.81[CEU][hapmap]
rs10201480	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs10205169	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11677303	0.80[ASN][1000 genomes]
rs12691633	0.91[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12994651	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13012748	0.91[CEU][hapmap];0.80[ASN][1000 genomes]
rs13382235	0.85[CEU][hapmap]
rs13385180	0.91[CEU][hapmap]
rs13392919	0.81[CEU][hapmap]
rs13398962	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13401617	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13405280	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13408764	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13412878	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13418304	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13420312	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs1375607	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1449491	0.82[CEU][hapmap]
rs1449502	0.91[CEU][hapmap];0.80[ASN][1000 genomes]
rs1562705	0.80[ASN][1000 genomes]
rs16847971	0.91[CEU][hapmap];0.80[ASN][1000 genomes]
rs17832157	0.82[CEU][hapmap]
rs1982384	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2044731	1.00[YRI][hapmap]
rs34199884	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34725547	0.80[ASN][1000 genomes]
rs35975765	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4267463	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4662401	0.89[CEU][hapmap]
rs62155635	1.00[ASN][1000 genomes]
rs6749591	0.91[CEU][hapmap]
rs7574284	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7586590	0.81[CEU][hapmap]
rs895935	0.80[ASN][1000 genomes]
rs956799	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs956800	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9630925	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997274	chr2:142760393-143599193	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv526107	chr2:142768518-142884248	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv875254	chr2:142833327-142931146	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1006247	chr2:142851056-143289465	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142857400-142862800	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr2:142858000-142861200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:142858800-142861400	Weak transcription	Brain Germinal Matrix	brain
4	chr2:142858800-142861600	Weak transcription	Hela-S3	cervix
5	chr2:142859000-142861000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:142859800-142861400	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:142860000-142861000	Weak transcription	Brain Substantia Nigra	brain
8	chr2:142860000-142861200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:142860000-142861200	Weak transcription	Brain Anterior Caudate	brain
10	chr2:142860000-142861400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:142860800-142863000	Enhancers	Brain Angular Gyrus	brain

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