Variant report

Variant	rs12478718
Chromosome Location	chr2:58258689-58258690
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:58257859..58260468-chr2:58264282..58266737,2	MCF-7	breast:
2	chr2:58250871..58252381-chr2:58256903..58259495,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10171955	0.82[ASN][1000 genomes]
rs10188390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10210198	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10496085	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10496086	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10496087	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1078191	0.89[EUR][1000 genomes]
rs11898024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12465171	0.94[EUR][1000 genomes]
rs12467842	0.92[EUR][1000 genomes]
rs12469522	0.85[EUR][1000 genomes]
rs12470851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12471043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12473840	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12475192	1.00[CEU][hapmap]
rs13386389	0.88[EUR][1000 genomes]
rs1371212	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1401101	0.82[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1518403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17049262	0.85[CEU][hapmap]
rs17049272	0.82[CEU][hapmap]
rs17049273	0.85[CEU][hapmap]
rs17049278	0.85[CEU][hapmap]
rs17049299	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17049308	0.81[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17049312	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17049314	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17049316	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17049321	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17049394	1.00[CEU][hapmap]
rs17049416	0.85[CEU][hapmap]
rs17049417	0.85[CEU][hapmap]
rs17830749	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2118897	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs34191187	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35876471	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3771203	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55723561	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55856965	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61548822	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6545679	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6732965	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67484511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6755324	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs72808498	0.87[ASN][1000 genomes]
rs72808501	0.87[ASN][1000 genomes]
rs72810305	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72810306	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72810307	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72810308	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72810316	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72810317	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72810318	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72810320	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72810323	0.97[EUR][1000 genomes]
rs72810325	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72810332	0.88[EUR][1000 genomes]
rs72810334	0.89[EUR][1000 genomes]
rs72810337	0.86[EUR][1000 genomes]
rs728574	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558693	0.85[CEU][hapmap]
rs968850	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[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	nsv834159	chr2:58101262-58283655	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv874200	chr2:58163178-58262016	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv999591	chr2:58214871-58316147	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58249600-58259800	Weak transcription	Ovary	ovary
2	chr2:58251400-58272000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr2:58251600-58258800	Weak transcription	Primary B cells from cord blood	blood
4	chr2:58255600-58267600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:58256600-58271800	Weak transcription	Left Ventricle	heart
6	chr2:58256800-58272800	Weak transcription	Adipose Nuclei	Adipose
7	chr2:58256800-58273000	Weak transcription	Pancreas	Pancrea
8	chr2:58257200-58259600	Weak transcription	Spleen	Spleen
9	chr2:58257800-58260000	Enhancers	NH-A	brain
10	chr2:58258000-58259000	Enhancers	GM12878-XiMat	blood
11	chr2:58258200-58259000	Weak transcription	Osteobl	bone
12	chr2:58258200-58259800	Weak transcription	Psoas Muscle	Psoas
13	chr2:58258200-58271800	Weak transcription	Brain Substantia Nigra	brain
14	chr2:58258400-58259400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:58258400-58260800	Enhancers	Primary B cells from peripheral blood	blood
16	chr2:58258400-58273000	Weak transcription	Liver	Liver
17	chr2:58258600-58272000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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